There are just too many! I'm a movie collector, and have most all of them. VHS, Laser Disc, DVD, and BlueRay. My favorite aviation scene is still the B-36 takeoff in Strategic Air Command
We gotta play by the rules, the thread says Top 5.
My main criteria for aviation movies is actual aireal footage.
The Spirit of St Louis is an exception because of the story and
Hells Angels probably ought to be in there but we only get five.
The Great Waldo Pepper is one of the best because it's most likely the last actual Curtiss JN-4 air to air we're ever going to get. Frank Tallman was responsible for most of that stuff and if he hadn't been killed in the filming of
Flight of the Phoenix we'd probably have been blessed with much more of that kind of stuff.
Strategic Air Command is one of a few 50's era films that use lots of spectacular USAF footage.
The key is real footage, films like
Red Tails and
Pearl Harbor that are 100% CGI just cannot compare to an older fim such as
Tora Tora Tora. The images don't convey the sense of flight properly, they can't adequately portray the extreme spatial separation and three dimensional oddities that real flight involves.
You really have to be there to get it.