Not comedies, but powerful romance titles:

Kimi Ga Nozomu Eien
Kanon

(both very sad titles)

with AYA and Love Hina you've already seen the best in the romance/comedy genre, though these are good too:

Vandread 1st and 2nd stage
Onegai Teacher and Onegai Twins (these aren't really comedies but they are funny).
Mahoromatic