I was even ready to rate Bakuman. 2nd Season lower if there was at least some other firm masterpiece in my opinion, but, alas. Another borderline masterpiece that I enjoy is Boku wa Tomodachi ga Sukunai . Decided to finally drop all those childish Digimons and Battle Spirits and the like as I don't like their openings anyway.
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.