|Deep Love - Ayu no Monogatari made me cry for over five minutes until I calmed down. The noisy kind of sobbing too, not a silent watering of the eyes like normal. D:
Naruto made me cry twice...
Spoiler (mouse over to view)
The first time was after Jiraiya died and Naruto was looking at the twin Popsicle and sitting all alone on the bench. That was super depressing. His death hadn't hit me hard until then...
The second time was when Naruto got to meet his mom, but those were mainly tears of happiness. And bittersweet too... he missed out on having an awesome family.
Vampire Hunter D: Bloodlust managed to make me cry tears of happiness too.
And then there's Guilty Crown, which made me sob a bit, and Mahou Shoujo Madoka Magica made me tear up.