I can't believe you didn't list the obvious...Vader dying in ROTJ...Yoda dying? Ben dying? Helloooo?
Actually, Buffy the Vampire Slayer has made me cry several times (no jokes about your opinions of the show) I've really gotten into that and Angel, so, when things happen I feel somewhat affected emotionally.
Some of these were when I was a bit younger...
Patch Adams.
What dreams may come. (I'm a sucker for Robin Williams I guess.)
The Truman Show.
The original King Kong. I was so sad when the planes killed him.
Baby. (It was a dinosaur movie of sorts...was a part where the daddy dino gets killed by the bad guys.)
The Patriot. (mel gibson...not segal.)
The Last Unicorn.
The Mask of Zorro.
I'm sure there are lots more...I am a big wuss.