A few that haven't been mentioned yet (though not necessarily my favorite)
Flyboys
Decent amount of flight scenes, not-so-great story.
The Red Baron
Good but few fight scenes, and apparently lame story (never watched it)
The Final Countdown
So, this modern aircraft-carrier enters some storm which takes it back in time to 1941, and they have the opportunity to stop Pearl Harbor from being attacked. Apparently there were some near-fatal accidents during filming (you can imagine why).
Russian Historical Detective (TV series)
Wish I knew more about this one.
Sky Fighters
Apparently a good film (in French) and from the looks of it, surreal flying scenes
Flight of the Phoenix (remake)
Not great, but fun - I liked it
Battle of Santa Cruz (Japanese Documentary)
Well done animation, but I can't speak Japanese
I don't know what this is, but I believe it's Japanese as well
For those we love(Warning:contains gore)
Good flying scenes, and even bases some effects from wartime footage. Controversial film because it apparently glorifies the Kamikaze suicide attacks.
633 Squadron
Good flying scenes, but lame effects. I don't know how good the movie is.
Anyway, it's also famous for this parody:
Tora Tora Tora
Film about the attack on Pearl Harbor. Good overall, way better than the Bruckheimer/Bay version.
Amelia
Airplane!
Who hasn't seen this one
The Rocketeer
Another Sci-Fi, but it's got interesting flying scenes with a Gee Bee racer.
The Strategic Air Command
With Jimmy Stewart and real B-36s
Those Magnificent Men in Their Flying Machines
Great movie
The Right Stuff
Great film about the early years of the American Space Race
The Great Waldo Pepper
I only vaguely remember seeing this. Apparently it's also a great movie
The Spirit of Saint Louis
Again with Jimmy Stewart. Good film.
That's all I got for now