DeGeneres' eponymous show won in the best talk show episode category for "Ellen and Portia's Wedding Day," which chronicled her August nuptials to the Better Off Ted star.
"In my opinion, we are not fighting for gay rights, we are fighting for equal rights," DeGeneres said at the show.
Housewives won comedy series, while its Sunday-night buddy Brothers & Sisters nabbed drama series honors. The New Adventures of Old Christine's "Unidentified Funk" took home the award for outstanding individual episode.
Two special recognition awards were doled out: one to the now-defunct L Word and one to Funny or Die's Prop 8: The Musical. The musical number was performed at the Saturday ceremony.
D-Lister Griffin, donning a skimpy bikini, was given the Vanguard Award.
Other winners include Milk, for best feature film, and the Rev. V. Gene Robinson - the first openly gay Bishop of the Episcopal Church - who received the Stephen F. Kolzak Award.