When Kamina died in Gurren Lagann- that had me crying, which wasn't too good because I was in Math class.
I didn't cry for Asuma until Shikamaru got revenge on Hidan, then the waterworks really got started.
I bawled for Hughes, but that's to be expected. But still, that wasn't cool.
No matter how many times I watch it, when Lavi fights himself in his mind I end up sobbing and hugging my computer screen.
Lenalee's monologue of her life being a dream in one of the last episodes of DGM also makes me bawl, though not usually to the extent of Lavi's fight.
When I was little, when Heero apparently blows himself up in his Gundam, that made me howl so bad. That was probably because I had a little-girl crush on him, though. That may not be exactly what happened, but I distinctly remember watching Heero, there was a detonator involved, and I was crying "NO HEERO DON'T DO IT!"
That's all I can remember, though there are probably a few more.