Ach, JZ beat me to it on The Fountain. Great movie, moved at a stately pace that I liked. Not every movie has to be fueled by caffeine, sugar, adrenaline, and cocaine. On the same note, the remake of Solaris was very, very good. Deeply under-rated. People who wanted action sci fi didn't like it because it was too cerebral, and film snobs didn't like it because they all insisted that the six hour russian version was better. But I loved it. Neither make my top 5, but still very nice. Close Encounters of the Third Kind goes here, too. I put these in the Exploration of the Unknown category, along with the movie that DOES make my top 5: 2001: A Space Odyssey.
Inception is another one of those late-90's (I know it was filmed in the 2000s) movies about cartesian doubt. Right along with the Truman Show, Dark City, and the Matrix. They all have something to recommend them, but Inception appeals to me because I like a good heist movie. Some other cartesian movies include Total Recall, Eternal Sunshine of the Spotless Mind, and Momento -- though those are more about questions of identity than reality.
Star Wars took a harsh beating due to the prequels, and I've no doubt it will suffer from the new movies, if for no other reason because Disney is apparently going to invalidate a huge swath of EU canon. But the original movies are still great. I plan on introducing this to my daughter when she's old enough by using Machete Order: Eps 4, 5, 2, 3, 6. Star Trek is OK, Serenity was a fun ride, etc etc etc., but Star Wars is the Holy Trilogy for a reason. While Starship Troopers the book was written as political/social, Veerhoeven's film tried to be a critique of the book but ended up being a fun but mindless adventure story. Weird Science was a fun romp, but I'll mention it mainly because Claudia Christian claims she and Kelly Le Brock hooked up and.... mmmmhhhh....
Tron is one of those movies (and I'm talking about the original here) because it works on so many levels. Filmed in the era of the Apple ][, it actually makes MORE sense in the internet age. The issues of hierarchical vs distributed control it explores are very relevant today. Hell, even more now with the NSA scandals. I categorize it as a "rabbit hole" movie where the character goes to a different universe and has an adventure, which gets juxtaposed with their mundane life in our world, as opposed to the Cartesian Doubt movies, where the question of which reality is really real is primary. Other Political/Social movies include District 9 (though arguably that's transhumanist, it's too thinly veiled social commentary to be really relevant), Equilibrium, Logan's Run, Ghost Busters, War Games, Gattacca, Real Genius, and lots more.
There are lots of good Time Travel movies. Back to the Future gets my vote, though the sequels don't do it any favors. It's just plain a fun adventure. Some honorable mentions: Terminator was great but its EU hurt it and I don't like its fundamentally anti-technology message. Most movies punt on the mutability of history and how to resolve paradoxes. Bill and Ted's Excellent Adventure is unique in being the first time travel movie to be entirely internally consistent and paradox-free. Most authors prefer the Terminator/12 Monkeys/Time Cop approach where the characters travel back in time to change history and end up creating it. I haven't seen Primer, but I've heard a lot about it and want to; however, I think they miss the fact that despite their careful attempt to dodge the problem, they STILL can't avoid paradoxes. I can explain if someone really cares, it deals with some deep social sciences/information theory issues rather than physics.
Then you get the transhumanist movies. None make my top five, though I love the concept. Those are movies that explore the nature of humanity and what is human. You get silly takes on it like Species and Fifth Element (both of which I really hate), plus Howard the Duck and Twins (yes, really, and both of which I actually like quite a lot). Short Circuit is silly, while . Robocop falls into this genre, as does the truly awesome Blade Runner. And horror stories like The Fly.
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