Difficult to pick a single fave. Here are the games I've spent most of my time playing back then.
On PC:
- X-Wing series (X-Wing, TIE Fighter, etc.)
- Star Control 2
- Earthsiege 1 and 2
- Starsiege: Tribes
- Team Fortress mod for Quake
- EverQuest
On arcade, mostly fighting games, and some side-scrollers:
- Mortal Kombat 1, 2, 3, 4
- Killer Instinct 1 and 2
- Virtua Fighter 1 and 2
- Marvel Vs. Street Fighter
- TMNT
- X-Men: Children of the Atom
Want to go back to the 80s? Lode Runner, Rescue on Fractalus! and Karateka. Also Gyruss introduced me to modern remixes of classical music.