I cried at the end of Fooly Cooly.
For a totally odd and humorous anime meant to parodize the government and pop culture, it ended beautifully.
The Evangelion Ending (whether Movie or Series) was amazing. Also the part where[spoiler] Eva 03 was eaten by Shinjis Eva and almost killed his friend, or when his body melted and he lived a few hours on the telepathic plain.[/spoiler]
And I agree with the Fullmetal Alchemist.
Off the topic of anime, the dog episode of Futurama.
Dick move guys, Dick move.