the Anime Frutis basket had such a lame ending, i didn't cry :/
The manga however did make me cry
Anyways. I didn't read back through the posts, but I'm sure these are already mentioned:
Air (TV)
Kanon
Clannad (including after story and the movie)
Code Geass (Such a tear jerker...

)
Bokura ga Ita
Grave of the Fireflies
Kenshin OVAs
5 cm. per second
Saikano
h20 - Footprints in the sand (sorta)
Kimi ga Nozomu Eien AKA Rumbling Hearts
Yeah... i never really cried on anything. Besides the first three. And pokemon... all the time
But they all have their sad moments