My overally favourites are whatever is good - I'm still playing Homeworld (with with obligatory B5/DS9 and Star Wars mods), shooters - Deus Ex, Max Payne (with the Matrixed mod, preferably, or at least Kung Fu 3) and space shooters.
My big shiny thing right now is the Freespace 2 game modded for Babylon 5. The main campaign is set in the Earth Alliance Civil War, but there is also a massive 37-mission In The Beginning campaign - OK, so it's sampled from the russian disk and the translations suck, but it is truly cool...there's just something innately satisfying about flying a Starfury/Thunderbolt and blasting Raiders/Clarke's troops/anyone who wants some...
"Whom do you serve?"
"The Truth"
"What is the truth?"
"That we are one people, with one voice"
"Will you follow me into fire, will you follow me into dartkness, will you follow me into death?"
"Yes"
"Then follow"
- Dukhat & Delenn, In the Beginning