Speilburg's "Always". I believe it is a remake of a war film but this is about water bombers in the late 80's. The opening shot of guys fishing in a boat as the Catalina (PBY) "lands" and scoops up water comming straight at them is one of my favorite aviation shots of all time.
(Yes, seaplanes do "land" on water.)
"Empire of the Sun" Ok, not realy an aviation movie but the slomo shot of the Mustang pilot waving at the boy brings tears to my eyes every time. Absolute magic.
Battle of the River Plate. Outstanding, ok only aeroplane is a "Sea Tiger" on a midships catapult, pretending to be a Shagbat.
Of course there is always "Midway", loved it.
Lastly don't forget "A Matter of Life and Death". Possibly the best movie ever made (about an RAF pilot, any way.) Still stong and relavant today.
PS, almost forgot, "Hunt for the Red October". Pity it was not true to the book and have "Two-seat Sea Harriers" and one of our flat tops but it did have interior shots of one of my company's F27s pretending to be something more warlike!