Yes a lot anime have made me cry but a lot are me cry do to me being happy. Angel Beats is one, Fairy Tail and Sword art online had a few that got to me.
Death Note
L and Light's Dad dyng got to me.
.
Code Geass the ending made me cry a little.
and Tengen Toppa Gurren Lagann
.
But i believe the one that got to me a lot was Strawberry Panic :'( the feels i had for that anime.