I was going to never rate comedies highly, but Lucky☆Star is more than a comedy, it's a meta-comedy and is enjoyable on many layers. Claymore is only slightly behind. Tengen Toppa Gurren Lagann and Bokura no definitely deserve a mention, but these are more flawed works.
Suzumiya Haruhi no Yuuutsu is revolutionary anime in several ways, so for me it has the upper hand over Black Lagoon which is also a great masterpiece, but in more mundane , complex and adult way. Lots of titles in Spring season, but I can't vouch for the rest.
Ergo Proxy is my favorite anime of the past which is still a full head ahead of most anime, though I see its imperfection nowadays. I also see Fate/stay night and Hellsing Ultimate as minor masterpieces deserving a mention.
Fall has become even more saturated than Spring lately. Beck is something unique that I'm willing to cherish. Genshiken is a cozy place to return to. Zipang is probably the best navy anime, at least to my awareness.