Why do so many people say Fruits Basket? Granted, Fruits Basket's ending was enough to make me cry, but saddest? Well, meh, here's some that made me cry:
AIR
Chrno Crusade
DNAngel
Elfen Lied
Full Moon wo Sagashite
Kannazuki no Miko
Kannon
Kimi ga Nozomu Eien
Ragnarok the Animation
Rurouni Kenshin OVAs
Saikano
Scrapped Princess
Wolf's Rain
I also thought AIR was sad too. It's one of the saddest animes ever, and I never really understood it. Also, Full Moon wo Sagashite was sad too. Especially the ending. I nearly cried.
You know, I completly agree, AIR made me cry really hard at the end, but maybe that was partly because I didn't understand it. When I composed myself a watched it again, I realized that the ending itself may not have been that sad, but to me it was like the last straw, the whole story was slightly depressing and maybe a bit touching, but not enough to make you cry, but the ending is so bittersweet and leaves you full of questions and further hopes for the character, it's like a dam breaking and I just cried, for a long time.