wayyy too many. It doesn't take much to make me cry...
Rurouni Kenshin OVAs
Azumanga Daioh--when Sakaki finds Mayaa and Mayaa protects her from the other street cats...i was BAWLING. I cried the entire episode. (hangs head in shame).
Saikano
Voices of a Distant Star
I cried at the end of Fruits Basket manga, not so much the anime
Nana (various points throughout), but especially during the first live that Nana sees Ren
...and there's more, just can't remember...