In my own brain, I see this list as the list of the most significant science fiction films, as opposed to the "best" or the most financially successful. This gives me latitude to, say, include films that are influential on science fiction filmmakers, but not necessarily the audience (or, vice versa, as the case may be).He's got a list of things he's already thought of (most of the obvious stuff), and is inviting comment at his blog.
The only thing I thought should definitely be on his preliminary list is anything by Terry Gilliam. I'm partial to Brazil, myself. Alas, I can't say that SF films are my favorite type of cinema ... often, I go out of my way to avoid them. (Though the upcoming Sky Captain and the World of Tomorrow does look intriguing.)
I hope that Scalzi includes a list or discussion of obscure SF movies worth seeking out. If such things even exist. The most obscure I can claim to have seen is Hombre Mirando al Sudeste (Man Looking Southeast), an Argentinian movie that is quite good until it is ruined by a far too literal ending.