And there are my picks from Donnie Darko and The Graduate

I know Mad World has been played to death in sad scenes on TV and movies, but the first I saw it was on Darko and it packed a punch. Very haunting, very effectively used in the film.
Mrs. Robinson was another that was used to perfection, I like how it was adapted for that scene in the Graduate. With the guitar chugging... down... slowly... as the car...
As to the composition of this list: I didn't do any instrumentals on mine. I made that choice in order to help me cut it down to 25. But I think we could have done two of these simultaneously, one with lyrics, one with just music. I could have complied 25 for each quite easily.
Oh, and when your done watching the Graduate with mom... pop on Last Tango in Paris. It'll be fun, trust me!
Would I steer you wrong?

(actually that would make a good LOC - top 50 uncomfortable movie experiences when watching with your parents or grandparents)