I think the September 15th sequence in Battle of Britian with the William Walton music is superb... Sod the computer graphics, real aeroplanes are what it is all about. Sadly, be hard to muster the opposition in such numbers these days.
Not so much a flying film but Catch 22 is a great, wondefully comic film and, I'd suggest, saviour of quite a few B-25 airframes!
Also "The Pursuit of D B Cooper" is worth fast forwarding through to just watch the sequences flown by Art Scholl in a duster Stearman... don't think there is any trick photography there (other than where the Aircraft is actually sitting on the car!). There's a momnet where even Scholl must have been thinking "yikes!" or similar!
As for Top Gun? Pah!