Surprise - although The Simpsons and Futurama were both nominated for Animated Program (Less than One Hour) (for "The Way We Weren't" and "The Sting", respectively - Futurama is eligible because the episode first aired after May 31, 2003), Fox's other prime-time cartoon, King of the Hill, got beat out by Samurai Jack ("The Birth of Evil"), South Park ("Christmas in Canada"), and SpongeBob SquarePants ("SpongeBob B.C.").
(The "one hour or longer" nominees, both of which can win as this is an "area" category (it's also possible to have no winner) are "The Powerpuff Girls: 'Twas the Fight Before Christmas" and the complete "Star Wars: Clone Wars" series, which, for whatever reason, is being treated as one episode rather than 25.)
The Simpsons has two other nominations: Alf Clausen, for Music Composition (Dramatic Underscore) for a Series (for "Treehouse of Horror XIV") Alf Clausen and Dana Gould, for Music and Lyrics (i.e. Original Song) (for "Vote for a Winner" from "The President Wore Pearls"). Futurama got a second nomination: Ken Keeler, for Music and Lyrics (for "I Want My Hands Back" from "The Devil's Hands are Idle Playthings").
These awards will be given out on September 12. Also, the Voiceover and Individual Animation Achievement awards, which don't have nominations (each entry is judged on its own merits), will have their winners announced sometime in August.
-- Don