There are a lot of these on the net. Why not one more? :-) I will try to keep this updated. Some commands are shell-specific (I use bash), and some are application specific, like the Apache commands.

a2enmod

enable apache module

a2dismod

disable apache module

a2ensite

enable apache site

a2dissite

disable apache site

apt-get

upgrades Debian/Ubuntu. Do sudo apt-get update first to update info, then sudo apt-get upgrade to get new version of installed files. To install a specific package, use sudo apt-get install foo, where foo is the package name.

alias

creates an alias of a command in the shell

awk

see gawk

cat

show / concatenates files

cd

change current directory

cd ~ / cd

go to home directory

cd -

go to previous directory

chgrp

changes a group of a file

chmod

changes the access rights of a file

chown

changes owner of a file

clear

clears the screen

cp

copies files

cut

cuts lines into (like @SubSet in @Forula)

date

shows the time and date

dd

convert and copy files

df

disk / partition info

dhclient

dhcp-client, use dhclient -r to release, and only dhclient to renew

dig

DNS entries

du

show directory / file sizes, use du -sh / to show total size and in “human-readable” form.

echo

prints characters

ed

text editor

emacs

text editor

exit

logs out (also CTRL-D)

fdisk

disk handling. Can list devices via fdisk -l

fg

moves a background program to the foreground

find

find files in the filesystem. Go to the directory where you want to find the file, use “find -name hosts” to find files named hosts.

ftp

file transfer utility (use scp or sftp instead)

fsck

filesystem check

fuser

shows who and what process is using a specific file or file system. Good when you want to unmount a drive. For example, fuser /media/cdrom shows the process and user that is using the cdrom and fuser -k /media/cdrom kills the associated process

gawk

reads records and fields from a file. Or words.

gpasswd

manages /etc/group

grep

searches a file for a regular expression pattern. grep -ir ‘johan’ .finds all files with the text johan, case insensitive and recursively

groupadd

adds a group

groupdel

deletes a group

gzip

compresses files

hcitool

configures BlueTooth connections. Use hcitool search to search for discoverable BlueTooth devices.

hidd

BlueTooth HID daemon. Use sudo hidd –connect XX:XX:XX:XX:XX:XX to connecto to a HID device

id

see your user id and group id’s

ifconfig

network configuration

info

show textinfo files

jobs

lists active jobs

kill

kills a process, use kill %jobno to kill a job. Some jobs may not respond to normal kill, you must use kill -KILL %jobno

less

show contents of files (backward / forward)

ln

creates a link between files

locate

find files in index

logout

logs out (also CTRL-D) or exit

ls

list files / directory

lshal

list HAL devices

lspci

list PCI devices

lsusb

list USB devices

mail

starts the mail program

man

shows manual page for a command

mkdir

creates a directory

mke2fs

formats drives

mkswap

sets up a swap partition

more

show contents of files (only forward)

mount

mounts a filesystem

mv

move or rename

nano

text editor

netstat

shows network connections

nice

handles process priority

ping

pings a host

procinfo

shows memory usage

ps

process status

pwd

print working directory

rm

removes a file

rmdir

removes a directory

passwd

sets log in passwd

route

set the ip routes

run-parts

runs all commands in a directory

scp

secure copy via ssh. Use ” and \ to escape filenames with spaces, like this: “HOWTO\ Create\ SSH\ Keys.txt”

sftp

secure file transfer (use scp if possible instead)

sed

stream editor, replaces strings in streams. Example cat test.txt | sed s/testing/helloworld/, replaces testing with helloworld in text.txt to stdout.

sensors

to read temperatures on motherboard, cpu etc.

shutdown

in SU mode, shutdowns the system, sudo shutdown -r now restarts the system.

sleep

sleeps the specified amount of time

sort

sorts the contents of a file

ssh

secure shell, use it like this: ssh username@host

su

goes to “super user mode” = root. In Ubuntu you have to set a root password first.

sudo

goes to “super user mode” on one command

swapon

activates a swap area

tar

binary to ascii encoder

telnet

telnet session, unsecure, use ssh instead.

top

monitors processes

touch

creates a new empty file or changes the date of an existing file

traceroute

traces ip hosts

tree

shows a tree of the filesystem

umount

umounts a filesystem

unalias

removes an alias

uname

shows information about the current system

unzip

decompresses ZIP files

update-rc.d

adds something to startup (Debian)

uptime

shows the uptime for the server

useradd

add a user

userdel

remove a user

usermod

modify a user

users

lists the users currently logged into the computer

vi

text editor

vmstat

shows memory usage

w

shows who are logged on and what they are doing

wait

waits for a job to finish

watch

runs a command every 2 seconds until CTRL+C

wc

word count. Also count lines

whatis

short explanation of command

whereis

shows where the specified command is and its related files

which

shows the path to the specified command

who

shows who are logged on

whoami

shows what user I am

write

sends a message to another user

xviddetect

setup video card for X

Xconfigurator

setup for X

Also see the good man-page-like command list at Oreillynet.