Oh. For some reason I thought this was the DOS-games-you-sometimes-return-to thread. In which case, Yeah, Aces of the Pacific gets a slot, and...I guess Carmageddon does too, but I think that was one of those DOS/w95 things. Whatever. Imperium Galactica, certainly.
Warcraft II, because duh.
Heroes of Might and Magic II, because duh.
Wing Commander III/IV, because duh.
X-Wing/TIE Fighter, because duh
While I no longer have any time for the C&C games, I did quite like C&C/RA when they were released. Even if I did have no talent for them.
Close Combat I/II, because holy ****, they almost made me into a wargamer. Almost. Damn fine tactical RTS, regardless.
The Jane's games, because jets, helicopters, missiles, bombs, explosions.
Various other titles I can't recall at the moment
Also, Mr. Mayor, I regret to inform you that you're clearly insane. B-17 Flying Fortress II came out well after SWOTOL and, as you might imagine, let you fly a B-17. Unless you meant SWOTOL was the last DOS sim that let you do that, I guess. In which case you're still crazy, but for totally unrelated reasons. Or something.