Probably listed already but I'm not going through 4 pages of bunk...
Wing Commander 1 and 2 (and their pairs of addon stages.)
Tie Fighter
X-Wing
Indiana Jones and the Fate of Atlantis
Commander Keen 1-6
(the ever classics) DOOM1/2, Heretic, and Wolfenstein-3D
Ultima Underworld
Star Control 1 and 2
Quake
Links386 (various versions)
M1A1 Tank Platoon
Hi-Octane
Magic Carpet 1 (not 2...2 sucks)
Prince of Persia 1 and 2
Dune 2
Command and Conquer 1+addon (still the only one I felt was perfectly balanced and fun)
Into the Eagles Nest
Infiltrator 1 and 2
Road Runner (arcade port)
Gauntlet II (arcade port)
Stunts
Leisure Suit Larry (in particular 6)
Comanche (1st one)
LHX Attack Chopper
...yes I'm aware the arcade versions of those type games are nicer, but they're damn fine for the day, real stand outs. Also WC1 and 2 are playable in WinXP if you can find Disc 1 of the 'Kilrathi Saga' ...2-4 are stupid Wing Commander 3 which stank.
I remember playing the hell out of that stuff, many more but those are coming to mind at this moment as I don't want to think over it for the next 30-60min looking up stuff.