Skip Beat!
Nodame Cantabile
Lucky Star
Azumanga Daioh
Moyashimon
Busou Renkin [sub]has comedy, though it's mostly action[/sub]
Love Hina
Bakemonogatari
Detroit Metal City [sub](I couldn't get into it because of the art, but it's comedy)[/sub]
Eureka Seven [sub](Not really comedy, but you should watch it)[/sub]
Full Metal Panic [sub](Second season:Fumoffu is mostly comedy, but first season still has some funny in it)[/sub]
Futakoi Alternative [sub](I remember this one being funny. I need to rewatch it as little else comes to mind)[/sub]
GTO aka Great Teacher Onizuka
Hayate no Gotoku
Hetalia
History's Strongest Disciple Kenichi
Kannagi
Karin [sub](I guess this can count as comedy)[/sub]
Ladies vs Butlers [sub](mostly fan service, but I found it funny)[/sub]
Lovely Complex [sub](might be a bit too sappy for you)[/sub]
Minami-ke [sub]and all of the sequel seasons.[/sub]
Mitsudomoe
Nyan Koi!
Overdrive [sub](sports mostly)[/sub]
Eyeshield 21 [sub](absurd shonen manga type sports)[/sub]
Popotan
Princess Lover
Princess Princess
Rosario+Vampire [sub](manga is much better, avoid second season)[/sub]
Sekirei [sub](Sekirei Pure Engagement is second season)[/sub]
Seto no Hanayome
Suzumiya Haruhi no Yuutsu aka The Melancholy of Haruhi Suzumiya
The World Only God Knows [sub](Currently being released, barely on episode 1 so far)[/sub]
To Aru Majutsu no Index
Tona-gura!
Toradora!
Trigun
VanDread
Working!!
Sayonara Zetsubou Sensei
Zero no Tsukaima
Kurenai [sub] This one isn't comedy, but you SHOULD watch it anyway. I thought it was really good.[/sub]
God damn, I'm tired, now.