SPOILERS SPOILERS SPOILERS!
Bellemere's death scene, particularly the "I love you" and that shot of Nojiko when Arlong's taking Nami away, where she's curled in on herself on the gound. Oh man, that gets me every time.
Chopper's past, especially the shot of him holding the mushroom out to Hiruluk when he's so beaten and bloody and you realize how much he went through, then later realizing the mushroom was poisened and you just felt so awful for him. Then after Hiruluk's death when Dalton's telling him to back off and not waste his life that way. And the shot of him waving Hiruluk's flag, begging Kureha to make him a doctor.
Sanji's departing scene from the Baratie mists me up, too, that was so well-done.
And the bit from 130, when Vivi tells them she can't come with them– the shot of Luffy's realization pangs my heart a little.
I'm sure there are more, but those are the ones that leap immediately to mind.