Gish, Cryptic Sea.
Aquaria, Ryan Gordon (via mercurial)
Quake III, id Software (direct zip d/l)
Quake II, id Software (direct zip d/l).
Quake, id Software (direct zip d/l)
0 A.D., Wildfire Games.
Rise of the Triad, 3DRealms
Ryzom, Nevrax (stopped business a few years ago ; the game is now supported by another company)
Seven Kingdoms, Enlight.
Arx Fatalis, Arkane Studio
Return to Castle Wolfentstein single player and multiplayer, id Software (sirect zip d/l).
MechCommander 2, Microsoft
No One Lives Forever 2, Sierra : toolkit contains the source code of the game
Wolfenstein: Ennemy Territory
Duke Nukem 3D, 3DRealms
Lugaru, Wolfire Games
Penumbra - Overture, Frictional Games, via git
Alien Swarm, on steam (the source code is available in the SDK (URL = steam://install/513 ; you might need to install Steam to get it)
This is not (by far) a complete list. Some old games have been removed (mostly Doom-generation and before), some other are missing (Allegiance ; anybody have a link on this one ? It seems it disapeared from MS Reasearch downloads ; Hexen, Heven II and Heretic: cannot find a reliable download site; The Operative - NOLF : went AWOL a few years back, the Wayback machine doesn't help much ; and so on).
Do not assume that this post is not connected to my previous entries. There are evil forces in this world you can't know anything about, and I'm in a deal with some of them.