Fun excercise, though I find it ironic that the page with this list features a gimmick of not being able to spell its own name or the “syfy” section properly. ;-)
I haven’t seen 12 Monkeys, Pi, Dark City, Children of Men, all of Altered States, Minority Report (I doubt it can be all that intelligent, being prejudiced against Spielberg/Cruise in that regard), Gattaca, or Moon.
Primer is good and intelligent.
The Fountain is too, in a different way.
So, I think, is Donnie Darko, also in its own way.
Contact I also liked and found intelligent. I might rate it a bit below those three.
The first Matrix was intelligent and cool… though also sort of super-heroic.
2001 I would call more artsy and interesting than strictly intelligent. Different kind of intelligence than I’d tend to measure when trying to brand a list as most intelligent sci fi films, maybe.
Quatermass and the Pit, I recall I enjoyed, but not as much as I liked the earlier Quatermass films. I thought they were more campy and fun than intelligent.
The Day the Earth Stood Still was cool in it’s day but I don’t know that it’s all that intelligent… I reserve judgement till the next time I see it.
I am kind of struck by how few intelligent sci fi films I can think of, even with the help of some web searching.
Other films I’d put up for consideration include Silent Running, Soylent Green, The Man Who Fell To Earth, Coccoon, Solaris (either), Colossus: The Forbin Project and A Clockwork Orange and in their way Alien, and Aliens.