3drealms	3D Realms FTP files (ROTT, Wolf3D)
archives	ftp.gamers.org pub/archives
doomworld	AtomicGamer doomworld/, now at doomworld.com/3ddownloads/
electronicarts	ftp.ea.com/pub select files
fileplanet	FilePlanet, PlanetQuake and other planet sites
frag-net	www.frag-net.com files, epicenter of pc gaming
freedoom	Freedoom releases
gamedesign	AtomicGamer gamedesign/
icculus		icculus.org projects and their files
idgames		Doom 1 engine stuff
idgames2	Quake engine stuff
idstuff		id Software's FTP files
librequad	LibreQuad files
lokigames	Linux game ports
lucasarts	ftp.lucasarts.com files (Jedi Knight)
openarena	download.tuxfamily.org/openarena
pooterman	www.pooterman.com files
qeradiant	AtomicGamer qeradiant/
quaddicted	quaddicted.com select dirs
quakerepo	quakerepo.net files
quakeunity	planetquake3/quakeunity.net files
ritualistic	ritualistic.com files
sierra		ftp.sierra.com select files
tastyspleen	tastyspleen.net files
telefragged	ftp.telefragged.com files
valvegames	Valve game related files (Half-Life, TFC)
westwood	Westwood FTP files
wolffiles	wolffiles.de files

All sorts of files related to id Technology can be found here.
There's also Westwood's FTP backed up. Westwood forever!