Well, it's belated, but better late than never. :-)
The Warzone 2100 team released version 2.1 of their continuation of the formerly-commercial RTS. The news link is broken for some reason. EDIT: And here is the fixed one. Well, the big 'hole' in WZ2100 has been the FMV that was in the original game, that comes in 2.2 I am told, but 2.1 is more stable and playable than ever (although I'm don't know the specific improvements over 2.0).
AssaultCube got a new website and a new release, version 1.0.2 which fixes a few glitches and brings some extra polish to the 1.0.x series of AC. Apparently Cube 2 (aka Sauerbraten) dev Eihrul has been backporting enhancements to AC, so looks much better than Cube 1, but I can't say for sure.
Speaking of Free FPS games, I thought this SuperTuxKart track, Sub-sea, being ported to Nexuiz was quite intriguing:
Speaking of SuperTuxKart, I can't remember if I mentioned or saw the 0.6rc1 release anywhere. By all accounts it's a massive improvement over 0.5 and the game is starting to realise a bit of it's potential. Version 0.7 will bring an overhaul of the graphics engine (port to Irrlicht from PLIB) and that plus all the new track development that is occuring, 2009 should be the year that STK becomes a showcase Free Software game. Still, the competition is getting tougher, but I hope that serves as motivation. :-)
Here's two questions for you, the readers, answers in comments please!
What was your favourite new project from 2008?
Which project do you look forward to new releases from this year?
For me, definitely Scourge (0.22 brings support for new model formats, which I think will make people pay more attention to it), with Vega Strike and UFO:AI releases also something I look forward to checking out.