Sitting around and shooting the scifi with Devilman and Paul, we came up with a few more appalling omissions to the EW list.
Donnie Darko: Okay, I hated this film, but Devilman says it's "the heir to the classic scifi cult movie tradition--so evocative it doesn't have to make sense."
Gattaca: One of the few recent scifi movies to take on a dystopian future that doesn't involve aliens and galactic wars, focusing instead on genetic testing and the human quest for perfection through science.
Invader Zim: Yeah, it's a cartoon, but it's a brilliant cartoon about a little green space man and his little green robot in a dog suit trying to take over the world. The artwork is amazing, and the show is a clever riff on the invading space alien trope--what if the space alien was only in third grade?
Stargate: Paul assures me this movie is "brilliant." I'll take his word for it; I'm still bitter that when the SciFi channel had to choose between the Stargate franchise and Farscape, it chose the Stargate franchise.