a

  alias    Create an alias •
  apropos  Search Help manual pages (man -k)
  apt-get  Search for and install software packages (Debian/Ubuntu)
  aptitude Search for and install software packages (Debian/Ubuntu)
  aspell   Spell Checker
  awk      Find and Replace text, database sort/validate/index
b
  basename Strip directory and suffix from filenames
  bash     GNU Bourne-Again SHell
  bc       Arbitrary precision calculator language
  bg       Send to background
  break    Exit from a loop •
  builtin  Run a shell builtin
  bzip2    Compress or decompress named file(s)
c
  cal      Display a calendar
  case     Conditionally perform a command
  cat      Concatenate and print (display) the content of files
  cd       Change Directory
  cfdisk   Partition table manipulator for Linux
  chgrp    Change group ownership
  chmod    Change access permissions
  chown    Change file owner and group
  chroot   Run a command with a different root directory
  chkconfig System services (runlevel)
  cksum    Print CRC checksum and byte counts
  clear    Clear terminal screen
  cmp      Compare two files
  comm     Compare two sorted files line by line
  command  Run a command - ignoring shell functions •
  continue Resume the next iteration of a loop •
  cp       Copy one or more files to another location
  cron     Daemon to execute scheduled commands
  crontab  Schedule a command to run at a later time
  csplit   Split a file into context-determined pieces
  cut      Divide a file into several parts
d
  date     Display or change the date & time
  dc       Desk Calculator
  dd       Convert and copy a file, write disk headers, boot records
  ddrescue Data recovery tool
  declare  Declare variables and give them attributes •
  df       Display free disk space
  diff     Display the differences between two files
  diff3    Show differences among three files
  dig      DNS lookup
  dir      Briefly list directory contents
  dircolors Colour setup for `ls'
  dirname  Convert a full pathname to just a path
  dirs     Display list of remembered directories
  dmesg    Print kernel & driver messages
  du       Estimate file space usage
e
  echo     Display message on screen •
  egrep    Search file(s) for lines that match an extended expression
  eject    Eject removable media
  enable   Enable and disable builtin shell commands •
  env      Environment variables
  ethtool  Ethernet card settings
  eval     Evaluate several commands/arguments
  exec     Execute a command
  exit     Exit the shell
  expect   Automate arbitrary applications accessed over a terminal
  expand   Convert tabs to spaces
  export   Set an environment variable
  expr     Evaluate expressions
f
  false    Do nothing, unsuccessfully
  fdformat Low-level format a floppy disk
  fdisk    Partition table manipulator for Linux
  fg       Send job to foreground
  fgrep    Search file(s) for lines that match a fixed string
  file     Determine file type
  find     Search for files that meet a desired criteria
  fmt      Reformat paragraph text
  fold     Wrap text to fit a specified width.
  for      Expand words, and execute commands
  format   Format disks or tapes
  free     Display memory usage
  fsck     File system consistency check and repair
  ftp      File Transfer Protocol
  function Define Function Macros
  fuser    Identify/kill the process that is accessing a file
g
  gawk     Find and Replace text within file(s)
  getopts  Parse positional parameters
  grep     Search file(s) for lines that match a given pattern
  groupadd Add a user security group
  groupdel Delete a group
  groupmod Modify a group
  groups   Print group names a user is in
  gzip     Compress or decompress named file(s)
h
  hash     Remember the full pathname of a name argument
  head     Output the first part of file(s)
  help     Display help for a built-in command •
  history  Command History
  hostname Print or set system name
i
  iconv    Convert the character set of a file
  id       Print user and group id's
  if       Conditionally perform a command
  ifconfig Configure a network interface
  ifdown   Stop a network interface
  ifup     Start a network interface up
  import   Capture an X server screen and save the image to file
  install  Copy files and set attributes
j
  jobs     List active jobs •
  join     Join lines on a common field
k
  kill     Stop a process from running
  killall  Kill processes by name
l
  less     Display output one screen at a time
  let      Perform arithmetic on shell variables •
  link     Create a link to a file
  ln       Create a symbolic link to a file
  local    Create variables •
  locate   Find files
  logname  Print current login name
  logout   Exit a login shell •
  look     Display lines beginning with a given string
  lpc      Line printer control program
  lpr      Off line print
  lprint   Print a file
  lprintd  Abort a print job
  lprintq  List the print queue
  lprm     Remove jobs from the print queue
  ls       List information about file(s)
  lsof     List open files
m
  make     Recompile a group of programs
  man      Help manual
  mkdir    Create new folder(s)
  mkfifo   Make FIFOs (named pipes)
  mkisofs  Create an hybrid ISO9660/JOLIET/HFS filesystem
  mknod    Make block or character special files
  more     Display output one screen at a time
  mount    Mount a file system
  mtools   Manipulate MS-DOS files
  mtr      Network diagnostics (traceroute/ping)
  mv       Move or rename files or directories
  mmv      Mass Move and rename (files)
n
  netstat  Networking information
  nice     Set the priority of a command or job
  nl       Number lines and write files
  nohup    Run a command immune to hangups
  notify-send  Send desktop notifications
  nslookup Query Internet name servers interactively
o
  open     Open a file in its default application
  op       Operator access
p
  passwd   Modify a user password
  paste    Merge lines of files
  pathchk  Check file name portability
  ping     Test a network connection
  pkill    Stop processes from running
  popd     Restore the previous value of the current directory
  pr       Prepare files for printing
  printcap Printer capability database
  printenv Print environment variables
  printf   Format and print data •
  ps       Process status
  pushd    Save and then change the current directory
  pwd      Print Working Directory
q
  quota    Display disk usage and limits
  quotacheck Scan a file system for disk usage
  quotactl Set disk quotas
r
  ram      ram disk device
  rcp      Copy files between two machines
  read     Read a line from standard input •
  readarray Read from stdin into an array variable •
  readonly Mark variables/functions as readonly
  reboot   Reboot the system
  rename   Rename files
  renice   Alter priority of running processes
  remsync  Synchronize remote files via email
  return   Exit a shell function
  rev      Reverse lines of a file
  rm       Remove files
  rmdir    Remove folder(s)
  rsync    Remote file copy (Synchronize file trees)
s
  screen   Multiplex terminal, run remote shells via ssh
  scp      Secure copy (remote file copy)
  sdiff    Merge two files interactively
  sed      Stream Editor
  select   Accept keyboard input
  seq      Print numeric sequences
  set      Manipulate shell variables and functions
  sftp     Secure File Transfer Program
  shift    Shift positional parameters
  shopt    Shell Options
  shutdown Shutdown or restart linux
  sleep    Delay for a specified time
  slocate  Find files
  sort     Sort text files
  source   Run commands from a file '.'
  split    Split a file into fixed-size pieces
  ssh      Secure Shell client (remote login program)
  strace   Trace system calls and signals
  su       Substitute user identity
  sudo     Execute a command as another user
  sum      Print a checksum for a file
  suspend  Suspend execution of this shell •
  sync     Synchronize data on disk with memory
t
  tail     Output the last part of file
  tar      Tape ARchiver
  tee      Redirect output to multiple files
  test     Evaluate a conditional expression
  time     Measure Program running time
  timeout  Run a command with a time limit
  times    User and system times
  touch    Change file timestamps
  top      List processes running on the system
  traceroute Trace Route to Host
  trap     Run a command when a signal is set(bourne)
  tr       Translate, squeeze, and/or delete characters
  true     Do nothing, successfully
  tsort    Topological sort
  tty      Print filename of terminal on stdin
  type     Describe a command •
u
  ulimit   Limit user resources •
  umask    Users file creation mask
  umount   Unmount a device
  unalias  Remove an alias •
  uname    Print system information
  unexpand Convert spaces to tabs
  uniq     Uniquify files
  units    Convert units from one scale to another
  unset    Remove variable or function names
  unshar   Unpack shell archive scripts
  until    Execute commands (until error)
  uptime   Show uptime
  useradd  Create new user account
  userdel  Delete a user account
  usermod  Modify user account
  users    List users currently logged in
  uuencode Encode a binary file
  uudecode Decode a file created by uuencode
v
  v        Verbosely list directory contents (`ls -l -b')
  vdir     Verbosely list directory contents (`ls -l -b')
  vi       Text Editor
  vmstat   Report virtual memory statistics
w
  wait     Wait for a process to complete •
  watch    Execute/display a program periodically
  wc       Print byte, word, and line counts
  whereis  Search the user's $path, man pages and source files for a program
  which    Search the user's $path for a program file
  while    Execute commands
  who      Print all usernames currently logged in
  whoami   Print the current user id and name (`id -un')
  wget     Retrieve web pages or files via HTTP, HTTPS or FTP
  write    Send a message to another user
x
  xargs    Execute utility, passing constructed argument list(s)
  xdg-open Open a file or URL in the user's preferred application.
  yes      Print a string until interrupted
  .        Run a command script in the current shell
  !!       Run the last command again
  ###      Comment / Remark

Commands marked • are bash built-ins
Many commands particularly the Core Utils are also available under alternate shells (C shell, Korn shell etc).

More bash commands: Linux Command Directory from O'Reilly, GNU CoreUtils.