Layla in Goodfellas.
Forrest Gump had a few good ones. When Jenny walks out the door listening to "Love Her Madly" from the doors "...love her as she's walking out the door." Always thought that was cheesy, but I liked it. Also, Free Bird when she attempts suicide. People don't always realize that was due to her praying as a child for God to make her "Free as a Bird, so she can fly. Far far away from here."
Dazed and Confused was perfect through the whole movie
Ferris Bueller. "Oh, yeah." And obviously Twist and Shout.
Wild Thing in Major Leauge
Bohemian Rhapsody in Wayne's World
Granted some of these, the song was actually part of the movie.