Toradora! is the queeen of tsundere and a great anime, but Tentai Senshi Sunred is one of the best parody comedies out there despite seemingly low popularity.
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.
Lots of decent works, none is good enough for me. If I really needed to choose, I'd probably go for Hachimitsu to Clover as with all its flaws it can still be nice at times.
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.