Oh man, so many. In the mid-'90s I loved Dark Forces, X-Wing, TIE Fighter, Doom/II, Descent, Duke 3D, Wolf 3D, Operation: Bodycount (a Wolf 3D clone with UN special forces and terrorists...and flamethrowers!), Raptor, the Hugo games, and pretty much any Apogee game I could get my hands on. I had a ton of those "1000 Games" type CDs, too. The Epic Megagames ones were the best.
Going further back, I loved Teenage Mutant Ninja Turtles even though it was RIDICULOUSLY difficult. Turns out it was also glitchy and broken and even if I had managed to get to level 3, it wouldn't have mattered anyway since you literally can't get past it without cheating (I didn't know there were cheats then).
Side story: my best friend had this old disk of BASICA games (which as best as I can tell must have been some kind of custom Friendlyware thing, as it had a Friendlyware-looking menu and some of the games--like Battleship--but also some that weren't on Friendlyware) that we played a ton of when his mom brought home a couple of old computers from work when they were upgrading equipment in the mid-'90s. ASCII graphics and everything. In particular there was a Pac-Man game that we played the absolute shit out of. Since losing the disk in the late '90s, I've found exactly zero information on the game until, by some amazing cosmic coincidence, a lot of old PC stuff I bought off a friend last year contained a disk that had the game on it. I'd seen some games that were *like* it, but different, but this was it beyond a doubt. Reunited after 20 years.