I've got a few
First time I cried was while I was watching Rurouni Kenshin when Kenshin says goodbye to Kaoru before he heads to Kyoto. Everything with that scene it's absolutely perfect and I cry every bloody time! I was in tears at the end of the first Kenshin OVA and I was crying the whole way through the second OVA, it was just too damn sad!!!! (Why couldn't the anime producers give Kenshin a happy ending like Watsuki-sensei gave him!! Of all the people in anime Kenshin deserved a happy ending!!!!)
The ending the Escaflowne tv series, it was such a beautiful series!!
Romeo X Juliet the ending was just....WAAAAAHHHH!!! You knew it was going to happen, but you just had this hope that maybe, just maybe it wouldn't be the tragedy that you know and then, it became even more tragic than the original play.
Gundam 00
When Lockon dies and basically the last half of the final episode of season one, I was just a mess
Code Geass, the last episode, around 14 minutes I'm complete mess, every time I watch it, the moment I hear Madder Sky start, I'm balling, and my glasses fog up. When I first watched it, I had to pause it to wipe my glasses so many times it was insane.
Now I did get upset at the deaths of Hughs, why did they kill him, it wasn't fair, I liked him!!! The end of Chrono Crusade was just heart wrenching. The last two episodes of Trinity Blood!! I did get upset at the end of Weiss Kruez Gluhen
Aya got stabbed or shot, can't remember and nobody is helping him as he is collapsing to the ground, no no no no
Ending of Last Exile. Also get caught up in the moving scenes from Naruto, just too many to list.
One last one that I just watched wednesday
in Bonen no Xamdou, Furiuchi takes off his own head, holy hell