Unix
SVGA Quake - Linux executable with SVGA Support!
X11 Quake - Linux X11 executable
glQuake - OpenGL Quake for Linux
TTY Quake - Text mode Quake for Linux!
Solaris Quake - For Solaris running sparc
Unix
Linux Client - for glibc systems
Linux Client - for libc systems
Linux Server - for glibc x86 systems
Linux Server - for libc x86 systems
Linux Server - for glibc alpha systems
BSDI Server - for BSDI 3.0 on x86
Solaris Server - for Solaris on sparc
...also make sure you get the skins!
Capture The Flag - Probably the best multiplayer modification for Quake. The only one I'm really ever interested in if I'm deviating from standard DM.
Star Wars CTF - Capture The Flag, but in different Star Wars scenes!
Quake Rally - Now this is really modifying Quake, a racing game!
Reaper Bot - The best Quake bot, you can play deathmatch offline.
CTF Bot - A bot for Capture The Flag.
Quess - Chess for Quake! Battle chess with the chess pieces being represented by different Quake characters.
Quake Soccer - Play Soccer in Quake online!
Rocket Arena - An exciting deathmatch mod that pits you against someone else in an arena.
YPOD - Your Path Of Destruction, a modification of Quake, to Doom!
Other popular mods that I don't care for, or never got into:
Team Fortress
ThunderWalker CTF
Air Quake
Pain Keep
Requiem
Expert Quake
Lava Ball
Quake-C Package - A nice Quake-C package. Features two versions of the compiler, a manual, etc.
WorldCraft - A very good Win32 map editor.
Quest - A popular DOS map editor.
BSP - Another popular Win32 map editor.
MedDLe - A freeware DOS & Win32 Quake model editor.
qME - The most popular Win32 Quake model editor, but very limiting shareware.
Quake Graphics Editing FAQ - Tells how to make textures & skins.
Wheel Utility - Win32 utility which allows you to use wheel mice in Quake.
Quake ...also available in a text file.
QuakeWorld Client
QuakeWorld Server
Quake Done Quick - A run through of the entire game in nightmare mode in 16.5 minutes!