My favorite game of that decade is actually still my favorite game today. System Shock. It was poorly marketed, and they made some release mistakes (like having a floppy version at all), but it was so far ahead of its time.
Baldur's Gate is definitely in my eternal favorite games list as well, even bought another copy of it on Steam a while back just so I'd have a reliable way to play it if I feel like it.
I loved the Wing Commander series, and Privateer 2 has a special place for me, as a save game editor I wrote for it is the only thing I've ever sorta 'published'. (Was included on May 1998 PC Gamer CD.)
Woo...nostalgia.