Oh man, I missed this thread before!
There's nothing girly about crying when you relate to an emotional moment of a good movie or show.
A lot of you have already listed these, but:
The Lion King
Toy Story 3
Pokemon: The First Movie
I've had more of these moments with shows than movies though. You have more time to really fall in love with the characters.
Pokemon - Pikachu's Goodbye, and the episode where you learn why Meowth learned to talk.
Buffy The Vampire Slayer - The Body
Just seeing this girl who's basically a superhero get completely broken when dealing with her mother's sudden death with absolutely no supernatural cause is really heartbreaking. She's used to being able to fight to protect the people she loves, but then this happens, and she has no idea what to do. It's an incredibly human moment, something this show always did really well.
Moments in television : Buffy the Vampire Slayer - The BodyTorchwood: Children of the Earth (short series of Torchwood)
Just all the things that happen to nearly all the characters, to the children, to Jack's daughter...
If you don't cry during this, it just means you don't have a soul.
Those are the big ones I was able to think of just now. There are others.