Quake3:
+ Lots of info and mods already released, there's probably a solution for your problem
+ Easy to get, sourcecode will probably be released soon so the mod can be released as freeware
- Bad graphics
- All possibilites are probably discovered already... It's harder to make something original for Q3

Doom3:
+ Excellent graphics
+ Really good physics and dound systems
- Doom 3 doesn't run really good at older video cards and less people have it
- It's relatively new, so there isn't as much info about it as about Q3