a2j                    alsa to jack connector
a2ping                 postscript to anything (like PDF)
a2p                    anything to postscript
a2ps                   anything to postscript
abcde                  CD to mp3 ripper
acidlaunch
ack                    advanced grep
advancecomp            recompression utility (better than pngcrush)
agave                  color scheme picker
aldo                   morse code tutor
amsynth                synthesizer (use it with [vkeybd] virtual keyboard through [jack])
antiword               word viewer
aosd_cat               display text in an on-screen-display (OSD) -- part of libaosd, an advanced OSD library
apg                    generate random passwords
apparix                bookmark directories (and use with "to", "bm", and "portal")
ardour                 non-linear audio editor
arecord                record audio from the soundcard
aria2c                 downloader
asciinema              asciicast terminal session recorder and viewer
atool                  Multi-format archive manager
audacious              music (mp3, mod) player
audacity               sound editor
audiotag               id3 tagger
base64                 better than uuencode
bashdb                 bash debugger
bmon                   network bandwidth monitor
boxes                  draw any kind of boxes around your text
brasero                cd/dvd burner
bsdiff                 binary differ
bspatch                binary patcher
btail                  a bayesian log filter
bvi                    binary vi (yet another hex editor)
cabel                  a graphical, modular synth interface to [csound] that's similar to [pure data]
calcoo                 calculator
ccx2                   curses xmms2 client
ccze                   log file colorizer
cdecl                  explain C declarations
cdstatus               rip and recover CDs and DVDs
cfg-update             like a smarter dispatch-conf
cg                     USENET binary decoder
chkrootkit             check rootkit
chmsee                 chm viewer
chronicle              Blogger client
chsuf                  change suffix of file(s)
clive                  download videos from youtube, etc...
codeviz                draw call graphs from C source
colorize               color log files
cookiecutter           Command-line utility to create projects from cookiecutters (project templates)
csound                 very flexible audio synthesis/programming system
csvmidi                convert csv files to midi
d4x                    downloader
dash                   small, ash-like shell
datamash               convert rows to columns, columns to rows, and other text operation swiss army knife
ddd                    interface for gdb
demoroniser            convert Microsoft characters to regular ascii
detex                  a filter to strip TeX commands from a .tex file
detox                  Safely remove spaces and strange characters from filenames
devilspie              match windows and take action (like xdotool)
diffbin                binary diff
diffuse                diff for X
discus                 color df
dispatch.conf          like etc-update (obsoleted by cfg-update)
djview                 text compression format like PDF (see djvu package)
dmenu                  convert stdin in to a menu
dnscache               DJB's caching only DNS server
doit                   a task management and automation tool
dosbox                 DOS emulator
dspspy                 sound activated recorder (obsoleted by listener)
dunst                  lightweight notification daemon
dvdisaster             dvd data backup and restore with error correction
dvipdfmx               dvi to pdf converter
easytag                GUI id3 tagger
ecasound               command line audio player, effects adder, and recorder
EditorConfig           helps developers define and maintain consistent coding styles between different editors and IDEs.
eix                    search portage (faster than esearch) (update-eix to update database)
eix-sync               do an "emerge --sync" and an "update-eix"
emerge-delta-webrsync  like "emerge --sync" but with deltas
enca                   guess and convert encodings
enfuse                 poor man's HDR
enscript               ascii -> postscript
ent                    test pseudorandom numbers
esearch                search portage (faster than emerge -s) (eupdatebd to update database) (eix is faster)
euse                   manipulate and query USE flags
evtest                 see the events generated in /dev/input/event* devices (part of the games-util/joystick package)
exiftool               view and modify metadata of various formats (including image formats and PDF)
exmap                  memory debugger and leak detector
faad                   AAC decoder
fasd                   Access/search recently/frequently used files on the command line
feta
fftw                   fast fourier transform library
firefox                web browser
firejail               Security sandbox for any type of processes
flagedit               emerge flag editor
flock                  manage locks from shell scripts
flux                   library
fontypython            font previewer
fotoxx                 image editor
frobtads               interactive fiction tads interpreter
frotz                  interactive fiction zcode interpreter
fulla                  fix lens distortion
fzf                    command-line fuzzy finder/searcher
fzf-z                  fuzzy finder/searcher for recently-used directories
fzy                    command-line fuzzy finder/searcher (better and faster than fzf, and written in C)
gcm                    GNU clipboard manager
g-cpan                 Gentoo CPAN emerge
gema                   macro processor (awk, sed, perl replacement)
get_flash_videos       Download youtube, vimeo, etc videos.
gflashplayer           Macromedia Flash Player
gforth                 forth implementation
gifsicle               animated gif creation tool
gimp
git-subrepo            Git Submodule/Subtree Alternative
gkrellm
gkrellm                graphic system monitor
glances                CLI curses based monitoring tool - like htop + iotop
glark                  advanced grep
glulxe                 interactive fiction interpreter that reads glulx blorbs
gmrun                  run commands from a popup window
gnochm                 chm viewer
gnome specimen         font previewer
gnotime                GTimeTracker - a combination of a stopwatch, a to-do-list manager and time-keeping/billing system
gozer                  tool for rendering arbitrary text as graphics, using ttfs and styles
gpicview               image viewer
grace                  x y plots
grasp                  development aid
gs                     ghostscript
gtk2fontsel            font selector
gtkpod                 ipod interface
gtktalog               CD/DVD catalog
gvd                    gnu visual debugger
gyach                  Yahoo instant messenger gui?
hexcurse               curses hex editor
hexer                  hex editor with a vi interface
hidden                 show hidden windows
htop                   enhanced top
ht                     binary/hex editor and diassembler (aka "hteditor")
httrack                website mirroring tool
hydrogen               drum machine
i3                     tiling window manager
iconv                  convert text from one character encoding to another (ex: from utf8)
ifm                    interactive fiction mapper
iftop                  network use top
indent                 code beautifier (pretty printer)
InkScape
inotail                like tail, but uses the kernel's inotify system to make it faster
iprint                 output hex/octal of chars on input
jack-keyboard          a nice virtual keyboard for jack
joy2chord              chording keyboard app (wirelessdreamer on #linuxice on freenode)
jpegoptim              JPEG optimizer
jpilot                 Palm Pilot PIM
k3b                    cd/dvd burner
k9copy                 copy DVDs
katmake                OCAML makefile generator
kchmviewer             chm viewer
kcolorchooser          Pick colors (hex)
kcontrol               KDE configuration (obsoleted by systemsettings)
kdenlive               non-linear video editor
kdesu                  run KDE programs with superuser privileges
kdialog                sort of like xmessage and zenity
kdiff3                 3-way diff for X
kedpm                  ked password manager
key-mon                shows keyboard and mouse activity in a window
kid3                   bulk id3 tagger
kile                   LaTeX development environment
klavaro                typing tutor
klibido                USENET binary downloader
kontact                PIM that uses korganizer for its calendar
korganizer             calendar program
kpdf                   KDE PDF viewer
kprof], [gprof         profiling
kprof, gprof           profiling
kuickshow              image viewer
kuroo                  emerge GUI
l2p                    LaTeX to PNG
lame                   creates mp3 audio files
liblame                mp3 creation library
libplot                plotting
lilypond               music typesetter (using TeX/LaTeX)
listener               sound activated recorder (unfortunately, reads directly from /dev/dsp)
lphelp                 printer info
lshw                   list hardware configuration
lxappearance           change X themes, mouse cursors, fonts
lyx                    desktop publishing system with a LaTeX back end
lzo
lzop                   a file compressor very similar to gzip.  lzop favors speed over compression ratio
maim -s                screen shot util (like scrot)
makeztxt               create a palm zTXT file from an ascii file
match_parens           match parenthesis and brackets in LaTeX and other code
mcurl                  download files in multiple parts via [curl]
mediainfo              display information about a media file
memprof                memory debugger and leak detector
midicsv                convert midi files to csv
mimms                  play mms files
mitmproxy              man-in-the-middle http(s) proxy -- great for debugging and reverse-engineering
mlterm                 terminal that allows the use of proportional fonts
mktemp                 safely create temporary files and directories
mmsrip                 download mms streams
mmv                    safely move/copy/append/link multiple files by wildcard patterns
mogrify                like convert from the [ImageMagick] tools, but converts in place
mpage
mpd                    music player daemon
mplayer                movie player
mpv                    movie player (fork of mplayer2)
msmtp                  SMTP client and plugin
msort                  sophisticated sort
mpsyt                  video downloader (mps-youtube)
musca                  tiling window manager
muse                   music sequencer
musescore              musical score editor
mutool                 work with PDF files (including view and modify PDF metadata)
mutt                   mail client
ncc                    debugging and source tracing C compiler (can also draw call graphs)
ncdu                   ncurses disk usage
netbrake               bandwidth limiter
netcdf                 netcdfg3 - array access for manipulating scientific data
nethogs                another network top
newsbeuter             RSS reader
nginx                  web server (fast, low resource use, easy to config)
ngrep                  network grep
ninjam                 make music with others over the internet
nitfol                 interactive fiction zcode interpreter
nl                     number lines
notify-send            brings up a dialog box containing a message (like a simple zenity or kdialog)
ntpq -c pe
ntpq -c rv
ntptrace
num                    number utilities for mathematics (sum, median, quartiles, standard deviation, and much more)
nyxmms2                command line xmms2 client
objconv                convert and disassemble object files
obs                    Record and Stream Live Video Content
od                     octal dump
ogle                   dvd player
okteta                 another nice gui hex editor
okular                 pdf, ps, ebook, and chm reader
oopadmin               change default printer and add fonts in OpenOffice
oprofile               profiler
optar                  print data on to paper - 2D barcode with error-correction
p0f                    passive fingerprint tool
pan                    newsreader (gui)
par                    reformat paragarphs (like comments)
patool                 Multi-format archive manager
pavuk                  web page/site mirroring
pdfinfo                view PDF metadata
pdiff                  pretty diff (in postscript) using wdiff
ped                    sed done right (with perl)
peek                   Simple animated Gif screen recorder
perf                   performance monitor
pfe                    forth implementation (very standard)
pinfo                  color info viewer
pipe.vim               pipe to vim and back out again
ploticus               plotting
plotutils              plotting
poster                 split a large poster in to smaller sheets
postfix                MTA
psbind                 smarter psnup (resize postscript files to print multiple pages on one sheet of paper) (can crop margins)
psdim                  optimize nup pages for pstops
psutil                 get information on running processes and system utilization
pup                    parse HTML on the command line (like jq for XML)
pv                     Pipe Viewer: a tool for monitoring the progress of data through a pipe
pydf                   pretty df (like discus)
qemu                   emulator
qmv                    batch rename files using a text editor (from [renameutils])
qodem                  modem program that can do serial, telnet, ssh, zmodem, kermit, etc
qt5ct                  qt5 style editor
qtads                  interactive fiction tads interpreter
quvi                   Download videos from youtube and lot of other sites
ranger                 curses file manager (uses vim keys)
rawstudio              process RAW files
rdiff-backup           like rsync, for doing incremental backups
readlink               find the full path of a file
realpath               find the full path of a file
recode                 like dos2unix and unix2dos, but with many more encodings
recordmydesktop        make screencast videos
regex-markup           logfile colorizer
remark                 regex-markup (colorize logfiles)
remind                 reminder service
reverse proxy grapher  Visualize how external ports are mapped to internal ones
rkhunter               rootkit hunter
rlwrap                 run any command with readline editint support
rosegarden             midi editor and recorder
rtv                    Reddit Terminal Viewer
safecopy               data recovery tool (better than dd)
sam2p                  convert various filetypes (like png) to others (like eps)
scan-build             static analysis tool (part of clang and llvm)
sc                     spreadsheet
scrot -s               screen shot util
serio                  upload files over the serial port using just echo
sfmike                 speakfreely - talk
sfspeaker              speakfreely - listen
shutter                A feature rich screenshot program
socat                  socket netcat
socklog                system and kernel logging services (like metalog)
soundtracker           tracker
sox                      audio swiss army knife / utilities
speakfreely            Voice over IP client
speedcrunch            calculator
sponge                 soak up stdin and write to a file (for stuff like set to edit in place)
squirm                 squid proxy module
ssh-copy-id              automatically create ~/.ssh/authorized_keys on remote machines
sux                    su while transferring X credentials (better than xauth)
swaks                  Swiss Army Knife SMTP; Command line SMTP testing, including TLS and AUTH
swfdec-player          Macromedia Flash Player (from the swfdec-gnome package)
swf_play               Macromedia Flash Player
systemsettings         kde configuration program (replacement for kcontrol)
tar                    archive files and directories
taskwarrior            task manager
testdisk               disk recovery, works directly on block device, using PhotoRec
TeX4ht                 convert TeX files to other formats
text2graph.pl          convert text to a graph
thcrut                 network discovery and fingerprint tool
tilda                  drop down terminal
timer_entropyd         populate linux random devices with extra entropy from various timers
timidity               MIDI player
trueprint              prettypinter
ttyrec                 terminal session recorder and viewer
tunapie                tune in to a Shoutcast stream (like streamtuner)
unbuffer               flush stdin (from expect)
uniname                checks for valid UTF-8 characters (use "uniname -V FILENAME")
urlview                finds URLs in a file or stdin then lets the user select one of the URLs and act on it
ups                    visual debugger
upx                    executable compressor
utimer                 countdown timer and stopwatch
uudeview               decode uuencoded files and more
valgrind               memory debugger
valgrind               memory debugger and leak detector
VirtualBox             Virtualization
vlc                    video player
vym                    mindmapping app
w3mir                  website mirroring tool
w3m                    text browser (ala lynx)
watch                  run a command multiple times and display the output (with differences highlighted)
Watcher                Run commands based on inotify events (an improved incron)
wavbreaker             split WAV files
whatmask               subnet mask calculator (OSX)
wmctrl                 control windows from shell
wmsmixer
wxhexeditor            nice gui hex editor
wyrd                   frontend for remind
x11rec                 record animated gifs of activity in X windows
x86info                CPU diagnostics
xautomation            Control X from command line and find things on screen (can simulate key pressing)
xchat                  IRC client
xchm                   chm viewer
xdg-open               open URL in $BROWSER
xdiskusage
xdotool                simulate key and mouse actions (like devilspie)
xdvik                  dvi viewer
Xephyr                 nested X display
xmlstarlet             parse XML on the command line (like jq for XML)
xmms2                  music player daemon
xpp                    GUI printing interface
xrestop                a top for X programs that shows resource usage
xsendkeycode           send key events to active window
xvst                   x video service thief (download videos from youtube, etc)
xxdiff                 GUI diff
xxd                    hex dump
yace                   Yet Another Chess Engine
yase                   Yet Another Search Engine
yaydl                  yet another downloader (for youtube, vimeo, etc)
youtube-dl             Download videos from youtube and lot of other sites
yq                     parse YAML on the command line (like jq for YAML)
zargs                  a version of xargs that makes the find command redundant (part of zsh)
zed                    very small and fast vi-like editor (part of zsh)
Zenity                 display GTK+ dialogs from shell scripts
zgrviewer              view and navigate graphviz files (Java app)
zoom                   interactive fiction zcode interpreter
zrun                   transparently uncompress bz2 and gz files to a temporary file and run a program on them
zynaddsubfx            great, complex synth
zz                     dynamic parser