So many to choose from, I did a search through my iTunes and it came up with ones like:
McLusky "Undress for Success"
Jay Reatard "Hammer, I Miss You" and "Night of Broken Glass"
All three are spectacular, but they're more singles than ep's. They all clock in at about 10 minutes. It is an intoxicating and thrilling 10 minutes (or less), but in my mind ep's should be between 5-8 songs, lasting around 15-20 minutes (maybe more, if the band tends to write longer songs). With that as criteria, I'd say my favorites (too hard to choose one).
TV on the Radio's "Young Liars" EP,
Against Me!'s "Crime EP" (the original, released on Plan-it-X)
Reptile House "I Stumble as the Crow Flies" (super obscure Dan Higgs pre-Lungfish band. emusic won't have it, but you will eventually find it on soulseek)
Bastard "Controlled in the Frame" (If you're into Japanese D-beat...)