Casshern Sins, Mushishi, and Popotan had plenty of moments that made me cry. Corpse Princess also made me cry, but only when I found out that my kegemaran character died for a saat time and wouldn't come back.
First of all: Fruits Basket. This had made me cry the saat most of anything I've seen in my whole life. Even so, some of those tears in that river I cried for it were joy and laughter.
I cried a few times during basically everything. At some point, I cried. I cried during Ouran once, during Soul Eater at some instances, during Black Butler plenty of times (that tunjuk would sometimes just make me out of nowhere tear up. Maybe from keeping my eyes open staring at the screen too long...), I think during Vampire Knight a couple of times, and even during Hetalia (the Revolutionary War gets me every time).
I think the only one I haven't cried during is Baka and Test... no wait, I cried on the episode "Me, Shouko, and Kisaragi Grand Park".
(If you're wondering [probably not] the thing that has made me cry the most is HetaOni. Since it's an RPG based on Hetalia, it doesn't really count as an anime. But the amount of tears that I cried during its 16 1/2 episodes could easily fill a fishbowl.)
Ok I teared up when 1 died, I cried in the revolutionary wars on hetalia, I think I cried a little at some scenes from fairy tail (mostly because i am so obsessed) and although it doesn't count as an Anime the saddest Anime associated thing ever is HetaOni I cried m eyes out...