1. Microprose's F-117A
2. DID's Total Air War
3. DID's EF2000
4. Graphsim's F/A-18 PSF
EDIT:
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5. Road & Track's Need for Speed SE (gold of original)
6. ID's Wolfenstein 3D
7. ID's DOOM
8. Microsoft's Age of Empires (original)
9. Lucas Art's Dark Forces
10. Microsoft's Gorilla, QBasic game which came with MS-DOS 6.22 I believe (the office favorite, right behind Links386).
Also spent a lot of time on Test Drive and Stunt Driver, but not so much to make the list.
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I don't feel these are better flight sims than the big boys Falcon 4.0 and Jane's F/A-18, I've just spent (and still spending) much more time with them because they better satisfy the Tom Clancy/Craig Thomas reader in me. The only thing keeping me from playing more F-117 is that DOSBox gets kinda slow on me as a mission progresses. I still love the limited-war picture-taking recon missions, maybe plucking a missile boat on the way out of a photo shoot.
EF2000 and TAW are still the closest and most current games I've found to satisfy my style of game play, although I very much appreciate F4 and F/A-18 for what they are. I keep a PC around just for playing F/A-18 under Win ME, at least for practicing Carrier traps at night and/or during a lightning storm.
Graphsim's F/A-18 PSF (AKA Hornet Korea) is also one of my all-time favorites and how I came to find SimHQ, only now am I filling that void with Jane's. HK/PSF has nice training videos and an excellent full-screen high-rez mission recorder, although I love JF/A-18's dark and menacing EF2000-like feel (the GUI music really helps to set the mood).
I'm much anticipating what LP comes up with in a Hornet (not stealth but I love it anyway), but I have enough right now to keep me busy for years.