I'll cry when it's a really well-done emotional movie/episode. A few off the top of me gulliver:

SPOILERS

American Beauty: The end where Lester is recounting his life in black and white and Spacey's narration is so ... transcendant. "You will someday."

Cyrano de Bergerac: The whole final scene

The Mighty: The scene where Max runs barefoot across town and breaks into the "labratory" where they were going to help Kevin ... and finds out its only a laundry room.

Man on the Moon: Andy's funeral and then when they have the bookend with Tony singing on stage and the camera pans over to the audience ... and Bob is standing there, grinning and teary eyed. The perfect note to end the movie.

Spirited Away: Started bawling in the theatre when Chihiro makes Haku remember his name and then again when she had to leave.

The Shawshank Redemption: The end, with the rain washing down. 'nuff said.

The Princess Bride: When Inigo kills Rugen. "I want my father back, you son of a bitch." Everytime.

Cowboy Bebop: The whole of "The Real Folk Blues Pt. 2". Even though I still say he probably survived, the emotion in the episode was ... permeating. Also, the end of "Hard Luck Woman" where Ed and Ein say goodbye.

[Scrubs]: Several episodes. The early one where J.D. deals with death for the first time with that "neat" old woman who chooses to die rather than go on dialysis.

The one with the heart transplant paitent who dies in her bed waiting for a heart and her "death" is a big musical number of "Waiting for My Life to Begin" and then Cox freaks out when he can't save her and asks J.D. if he'll be all right. And J.D. just keeps looking at her and goes "...yeah." with a tear in his eye.

And of course Ben. His character made me completely reevaluate Brendan Fraser as an actor. The first time I saw that episode, even though I knew what was coming, I bawled for about an hour afterward. Very powerful.

Futurama: Two episodes -- "The Luck of the Fryish", with Fry trying to reclaim his lucky seven leaf clover from his copycat brother Yancey. And then he thinks that Yancey took his name after Fry disappeared, only to find out that he named his firstborn after him. And then there's that clip of Yancey saying how his misses Fry everyday. So well done. I just wished they hadn't ended the episode with "Don't You Forget About Me". Kinda took away from the whole episode.

And "Jurassic Bark". Good ol' Seymour. It was just a plain great episode all the way through ("PROFESSOR! LAVA!!! HOT!!!!!!"), but seeing Seymour's devotion to that big loveable goof Fry is touching. Fry, by the way, may be the greatest idiot ever ... "I'm having one of those ... whaddyacall'ems. A headache. With pictures." "An idea?" "Yeah, that's it!"