Doom:
EDGE (Enhanced Doom Gaming Engine):
http://edge.sourceforge.net/
PrBoom:
http://prboom.sourceforge.net/
Project FreeDOOM, "Freedoom is a project to create a complete
Doom II-compatible IWAD file which is Free Software.":
http://freedoom.sourceforge.net/
Vavoom:
http://www.vavoom-engine.com/
Doom3D (Direct3D Doom port):
http://www.doomworld.com/doom3d/
Doom64 (the Nintendo64 version of Doom, now for pc!!):
http://dsv.newdoom.com/downloads.shtml
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Quake:
DarkPlaces:
http://www.icculus.org/twilight/darkplaces/
ZQuake (for QuakeWorld):
http://zquake.frag.mu/eng/news/index.shtml
FuhQuake (for QuakeWorld, ZQuake with improved graphics!):
http://www.fuhquake.net/
QMB:
http://qmb.quakepit.com/index.php
OpenQuartz, GPL Quake content project:
http://openquartz.sourceforge.net/
TyrQuake:
http://www.planetquake.com/tyrann/engine.html
FitzQuake:
http://celephais.net/fitzquake/
ezQuake (for QuakeWorld):
http://ezquake.sourceforge.net/
Twilight:
http://icculus.org/twilight/
Quake retexturing project (new site):
http://www.quake.de/q/retexturing/
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Quake 2:
KMQuake2:
http://www.geocities.com/knightmare66/
BeefQuake:
http://mrg.telefragged.com/beefquake/
EGL & LiteGL:
http://www.echon.org/
R1Q2 - R1CHs Hacked Quake II Client/Server Replacement:
http://www.r1ch.net/stuff/r1q2/
Don't forget R1GL, Quake II gl-renderer with .png texture
support!
Q2:ICE :: Quake 2 Increased Control Effectiveness:
http://q2ice.iceware.net/ (site seems to be dead)
Quake 2 Retexture Portal:
http://texture.dragonwerks.ca/
If you want to download them all by hand
Try:
http://slacker.home.cosmic-cow.net/textures/
For some Quake 2 textures packed in .pak file.
Quake2max Site now has a DM texture pack.
http://www.planetquake.com/quake2max/q2max_retex.shtml
Doesn't work out-of-the-box with other Quake II engines.
Needs some files deleted inside the pak file (hint.png, skip.png
clip.png, I believe, more than one copy of those files in .pak).
Textures are in .png format, not useable by most engines
(useable in Q2ICE, Quake2maX, R1GL (=the renderer), EGL, LiteGL)
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Hexen 2:
Hexen 2 Unofficial Patch:
http://sky.prohosting.com/pa3pyx/hexenii.html
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Blood:
Transfusion, multiplayer Blood on modified Quake engine:
http://transfusion.deathmask.net/
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Settlers II:
Widelands, similar to Settlers II, still in progress:
http://widelands.sourceforge.net/
That's about it.
Sorry about the long post.