BASH SHELL COMMANDS —

• && : Execute one command and then another.
• > : Output and overwrite contents.
• >> : Output and append contents.
• | : Used to redirect function output.
• alias : Used to create a mnemonic reference to a command.
• apt-get : On many Linux builds used to search for and install software.
• aptitude : Seems to be an alias for 'apt-get'.
• aspell : Spell checker function.
• awk : Used for find and replace with pattern matching.
• bind : Can be used to bind a key to a function.
• mv : Used to move or rename a file or directory.
• break : As with higher languages, to exit a for or while loop.
• builtin : Use to include a shell function within a command or function.
• bzip2 : Compress or decompress [file] command.
• cal : Display a calendar with current day highlighted.
• case : Similar to higher languages switch, will conditionally execute a command when [argument] matches [pattern].
• cat : Display the contents of a file.
• cd : Change directory.
• chgrp : Change file ownership to group.
• chmod : Change file permissions.
• chown : Set file ownership.
• chroot : Run a command from a different root directory.
• chkconfig : Used to query or set system services.
• cksum : Computes the CRC value of a file.
• clear : Will clear messages from the terminal display.
• cmp : Compare two files data and return any differences.
• comm : Compare contents (str) of two files line by line.
• continue : Used to jump to the next iteration in a loop.
• cp : Copy one or more files to a new location.
• cron : Daemon for executing scheduled tasks.
• crontab : Schedule a task to run at a later time.
• csplit : Split and output a file based on a context pattern.
• curl : Transfer data (or one file) to or from a server.
• cut : Cuts a file into different parts, a bit like using 'slice' on an array.
• date : View (or set with parameters) the current date and time.
• dc : Desk calculator program.
• dd : Can make an exact clone of an (unmounted) disk.
• ddrescue : Can recover data from damaged files.
• declare : Declare variables and assign values.
• df : Shows free disk space.
• diff : Compare two files.
• dig : A DNS tool to query and troubleshoot nameservers.
• dircolors : Use to setup colors for the 'ls' command.
• echo : Writes string parameter to STDOUT or can be redirected to a file.
• eject : Send an eject command to removable media.
• enable : Can be used to enable or disable builtin shell commands.
• env : Will display, set or remove environmental variables.
• eval : Evaluates a command or expression.
• exec : Executes a command.
• exit : Leave the shell.
• expect : Automates communication with an interactive application.
• export : Can be used to set an environmental variable.
• expr : Evaluates an expression and prints the result to STDOUT.
• fdisk : Create or resize disk partitions.
• fgrep : Can be faster than 'grep' if searching for multiple strings.
• find : Search for files.
• for : Execute 'commands' for each 'words'.
• ftp : Launches an FTP prompt.
• function : Declare a function.
• fuser : Identify the process that is using a file or socket and optionally kill said process.
• gawk : Same as 'awk.'
• grep : Search a file for a text match.
• groupadd : Can add a user security group.
• groupdel : Inverse of above.
• groupmod : Modify a group.
• groups : Print the group name a user is in.
• gzip : Compress or decompress a file.
• head : Specify a leading amount of a file to output.
• history : Display the command history.
• hostname : Use to print or set the hostname.
• htop : View system load per process.
• iconv : Convert the character encoding of one or more files.
• id : Print information about the current user.
• if : Conditionally execute a command.
• ifdown : Bring a network interface up or down (same as 'ifup').
• import : Capture a portion of an X server screen.
• install : Copy files and set attributes.
• ip : Show and set routing, devices and tunnels.
• jobs : Lists the active jobs.
• join : Use to join lines (from files or STDIN).
• kill : Kill a process by supplying its PID.
• killall : Kill a process by supplying its name.
• less : Format output to print one screen at a time for easier reading.
• link : Create a symbolic link to a file.
• local : Declare and set a variable within a function that has local scope.
• logname : Display the name of the currently logged in user.
• look : Display any lines prefixed by [string].
• lprint : Print a file.
• lprintd : Abort a print job.
• lprintq : List the print queue.
• ls : Lists the contents of a directory.
• lsof : Lists all open files.
• make : Used for recompiling a group of programs.
• man : Opens a manual page.
• mkdir : Creates a new directory.
• mkfifo : For creating a FIFO file.
• mount : Used to mount a filesystem.
• mtr : Network diagnostics including traceroute and ping.
• mv : For moving or renaming files and directories.
• mmv : Mass move and rename.
• netcat : Read and write across networks; scan server responses / headers.
• netstat : To view networking information.
• nice : Run a command with adjusted scheduling priority.
• nl : Write a file with numbered lines.
• nohup : Run a command with hangup immunity.
• notify-send : Program to send a desktop notification.
• nslookup : Used to query internet nameservers.
• open : Open a file in its default application.
• op : Control user access to certain root applications.
• passwd : Updates a user password.
• ping : Test a network connection.
• pkill : Kill a process by supplying a full or partial name.
• popd : Use to traverse back down a path.
• pr : Prepare files for printing.
• printf : Format and print data.
• ps : Process status.
• pwd : Print the working directory.
• quota : Reports disk usage and limits.
• ram : Access RAM in raw mode.
• rar : For compressing and archiving files.
• rcp : Use to remotely copy files between two machines.
• readarray : Read from STDIN into an array variable.
• readonly : Specify a variable or function as read only.
• reboot : Reboot the system.
• rename : Use for partial renaming of files. Not a Bash builtin module.
• return : To exit a shell function.
• rm : For removing a file.
• rmdir : For removing directories.
• rsync : Remote file copy.
• screen : Multiplex a terminal across several processes.
• scp : Securely copy remote files.
• sdiff : Use to merge two files interactively.
• sed : Stream editor for basic text transformation.
• select : Select [value] in [words].
• seq : Output a sequence of numbers with an optional step.
• set : Set or unset shell variables.
• sftp : SFTP program.
• shift : Shifts parameters to the left.
• shopt : Set on unset shell options, such as 'checkwinsize', etc.
• shutdown : Shutdown or restart the machine.
• sleep : Pause or delay for a specified time.
• slocate : Restricted (and secure) file searching.
• sort : Sort, merge or compare lines from input.
• source : Also the dot operator, will read and execute commands from a file within the current shell context.
• split : Split an input into fixed size pieces.
• ssh : Open a secure shell client to login and execute commands on a remote machine.
• stat : Displays file or file system status.
• strace : Traces system calls or status.
• su : Substitute user identity.
• sudo : To execute a command as another user.
• sum : Calculate a checksum, but prefer 'cksum'.
• suspend : Suspends the shell and awaits SIGCONT.
• sync : Write any buffered data in memory to disk.
• tail : Selectively output the last part of a file.
• tar : Add to, list or extract files in an archive.
• tee : Redirect output to multpile files (useful for saving a copy of commands / responses).
• test : Evaluate a conditional expression.
• time : Loads a utility to measure the running time of another program.
• timeout : Run a command with an exit time limit.
• times : Will output both the user and shell time.
• touch : Strictly, change the stamptime of a file. Generally, create a new file.
• top : Find & view CPU intensive processes running on the system.
• tput : Set terminal dependant capabilities, eg. color, position.
• traceroute : Print the route packets take to a network host.
• trap : Run a command once a signal is set.
• tr : Translate, squeeze and delete characters from the input.
• true : Gives true (exit status 0), though the ':' colon command will do this faster. In essence, do nothing successfully.
• tsort : Performs a topological sort from a file or STDIN.
• tty : Print the name of the terminal connected to STDIN.
• type : Describe a command for a name.
• ulimit : Limit a user's access to system resources.
• umask : Can be used to automatically set file permissions on newly created files.
• umount : Unmount a drive or device.
• unalias : Unset a command alias.
• uname : Print system information.
• units : Convert units from one scale to another.
• unrar : Extract uints from a .rar archive.
• unset : Remove variable or function names.
• unshar : Unpack a shell archive script.
• until : Conditionally execute commands.
• uptime : Report uptime.
• useradd : Create a new user or update default information.
• userdel : Delete a user account and associated files.
• usermod : Modify user account information.
• users : Prints a list of the currently logged in users.
• uuencode : Encode a binary file for transmission over networks that only support it.
• uudecode : Decode a file encoded with 'uuencode'.
• vdir : Verbosely list directory contents, prefer 'ls -la' for more detail.
• vi : Launch the visual editor (http://ss64.com/vi.html).
• vmstat : Reports statistics on virtual memory usage and overheads.
• wait : Wait for the specified processes to terminate and return their exit status.
• watch : Execute (and display) a program periodically.
• wc : Display line, word and byte counts.
• whereis : Search for a program in $PATH and standard install directories.
• which : Search $PATH for a program file.
• while : Conditionally execute commands.
• who : Print the users currently logged in.
• whoami : Print the information of the current user.
• wget : Retrieve a file via HTTP, HTTPS or FTP.
• write : Used to send a message to another user.
• xargs : Execute a command passing a constructed argument list.
• xdg-open : Open a file or URL in the user's preferred program.
• xz : Will compress or decompress .xz or .lzma files.
• zip : Package and compress archive files.

While this list is extensive it is not exhaustive.
All commands will have modifier flags available, for a comprehensive list on those details see : http://ss64.com/bash/