Some blasts from the past:
Red Baron, especially the VGA-version. I've wasted so many hours with that one.
Aces over Europe / Aces over the Pacific. The Red Baron engine put to use in WW2, that was truly awesome. Though in sheer fun it's surpassed by, indeed, Secret Weapons of the Luftwaffe.
'Modern day' games:
Crimson Skies. Utter, utter FUN.
IL2 Sturmovik 1946. The entire IL2 universe rolled into one game. Seriously, if you want a realistic WW2 game, there's only one choice. A tad difficult, but very rewarding.
MS Flight Simulator. Sorry, but I love it.
I didn't like the follow-up to Secret Weapons of the Luftwaffe (Secret Weapons over Normandy). Didn't have the same charm and Crimson Skies simply was way better and funnier.
Personal favourite though, by a long mile, is T.F.X. Simply because I understood it completely. I've tried modern military sims, like Lock-On and Falcon 4.0. Didn't get into it and, funnily enough, both games are re-released with all the numerous bugs fixed (Flaming Cliffs and Allied Force respectively). I feel a bit robbed now, owning the original games and me having to shell out more cash to get the fixed versions (so I didn't). If you want Lock-On or Falcon 4.0, go for Flaming Cliffs and Allied Force.