The only real emotional scenes I can think of, the ones I still feel a strong connection to, are from my childhood. I don't really get emotionally attached to movies anymore, although Scrubs always found a way to tear at my heartstrings (ie, How to Save a Life scene). Ones I remember from my childhood:
Land Before Time, when Littlefoot's mom dies. That was the first movie I ever cried over, a couple of scenes in that movie were devastating
Mr. Holland's Opus, when he sings 'Beautiful Boy' to his son. Similar thing would be October Sky
Empire of the Sun, when Jim's buddy is killed, but there are various points near the end that are emotional
More modern ones...The Pianist had a number of scenes that were truly emotional, the scenes between the Pianist and the German colonel were something I didn't expect.
Das Boot and Requiem for A Dream, two movies where I felt absolutely depressed after watching them. American History X was kind of the same way
Seabiscuit was cheesy, but I still liked the last scene. Ali was a movie that probably lasted too long, but there were two scenes in particular that were special. The first was when Ali was running and a bunch of kids showed him the murals they paintings of him. Also, the entire last fight scene was fantastic IMO.
That song is perfect