Star Control 2
The Jagged Alliance series
Wing Commander: Privateer
The Quest for Glory series
Heretic & Hexen
A couple of obscure ones:
Stonekeep: A first person RPG from the mid-90s, this game had a big production budget, but came out to mixed reviews at best, and didn't do to well financially. Truth be told, it's buggy as hell and probably not even a good game all things considered. But for me, it works well as a mood piece, and I played the heck out of it.
Lightspeed: A first person flight sim/space exploration game from the early 90s that I've mentioned a bunch of times on these boards, so I won't say too much about it, except to say that it needed five 5 1/4" floppy disks.
Laser Squad: A turn-based tactics game that was a predecessor to XCOM and the Jagged Alliance games; with only five missions, it's fairly bare bones, but those missions were quite difficult so I got a lot out of it.