My favorite use of classical music in a movie is the climactic scene in Man Facing SouthEast (or maybe it was SouthWest) which was a foreign film (brazilian perhaps? It is a pretty old film) involving a guy at an insane asylum who claims he is from another planet and eventually convinces the other asylum 'residents' that he is and even causes some of this doctors to wonder, even though he looks normal and really does nothing unsual. at the end there is a scene choreographed to the 'Ode to Joy' portion of Beethoven's 9th which is utterly joyful and fantastic and liberating. You have to see it to get it.
Ironically, another of my favorite moments is from "Immortal Beloved" where a young Beethoven runs to a local pond to attempot to escape and abusive home and as he floats in the pond beneath a starry sky with the stars reflected in the pond the soundtrack plays the Ode to Joy. In general that is a great movie using Beethoven's music very well.
Amadeus is very good, too, as long as you realize that it is primarily fiction and, if you are of a certain age, as long as you can get past the fact the Pinto is supposed to be Mozart.
Edit:
Here is a link for the first movie:
http://us.imdb.com/title/tt0091214/