Some good choices here! Impossible to say really, but in terms of hours spent and enjoyment, probably for me (and not in an order):
1. Halo 3 - still playing online after 18 months
2. Goldeneye - played this to death, and my first multiplayer FPS experience
3. Red Alert - loved the skirmishes, spent more time just on the map editor than most games
4. Dawn of War - just a totally solid RTS game, still play it now
5. Fallout 3 / Mass Effect - both were epic! Can't decide which one I preffered, although the ending of Mass Effect was definitely more memorable