Neon Genesis Evangelion for its' awesome depiction of emotionally wrecked cast of characters along with a few chessmasters (khmYuikhm).
Crest/Banner of the Stars for the awesome couple dynamic.
Shigatsu wa Kimi no Uso for the emotional rollercoaster and a fucked up parallel to a parent on a death bed pulling a very shitty attempt at something (nobody was killed in the attempt).
Still Cowboy Bebop. Original Macross remains a sentimental favorite since I grew up on it. ROD OVA, Azumanga get honorable mention. And while many people don't like it, RahXephon.