Best is always relative, especially when discussing movies as taste is an issue. Being an art form, there can never really be a "best". But since I'm the one writing this, you are stuck with my opinion because it's awesome.
Yeah, you watch that and tell me this isn't what your nightmares are composed of.
Alien/Aliens - The grandaddy of the Sci-fi Horror genre. James Cameron's sequel lives up to the original but lacks the atmosphere due to blowing off H.R. Giger and not allowing him onto the project due to Cameron's idiotcy.
H.R. Giger's Alien is the greatest monster ever created and captured on film, hand down. Anyone who disagrees needs to watch the entire series again.
Dark Star - The entire movie has a very, very chilling effect on the viewer even though it is technically a dark comedy. A cult classic through and through.
Young Frankenstein - "PUT. ZE CANDLE. BACK!"
Unbeknownst to most, Godzilla had a guest cameo in Waterworld
Waterworld - Kevin Costner as a fish.
Big Trouble in Little China - Everything in Mortal Kombat was stolen from this movie. Stars Kurt Russell!
The Thing - A great-survival-from-the-alien-thats-trying-to-eat-us flick. Imagine being eaten by your fellow Antartic scientist buddy. Now imagine that you have no hope of resque... Presenting, The Thing!
Silent Running - Hippies in space. Pretty disappointing when you start watching it and realize that it's exactly that.
Dark City - Don't mess with your tv, that's how the movie is supposed to look. John Murdoch struggles with his past as telekinetic badguys named The Strangers toy with his city and the people's lives within it.
Grindhouse (Planet Terror / Deathproof) - Robert Rodriguez and Quentin Tarantino do the unthinkable and film a tribute to 70's grindhouse flicks. It ends up pretty good. Everybody always complains about Deathproof's ending, but it was ended to be anti-climatic and have that not finished feeling.
ACK ACK! ACK ACK ACK ACK! ACK ACK ACK!
Mars Attacks! - The funniest Martians-invading-Earth flick ever.
Back to the Future - Marty McFly, with the aid of Doc Brown, successfully test time travel. Marty then screws with time itself, hilarity and a classic ensues.
Batman Returns - Tim Burton directs a batman flick. That should be enough, but for the hard to impress there's Micheal Keaton as Batman (Argueably the best movie Batman ever), Danny Devito as the Penguin, and Michelle Pfeiffer in a full body cat suit.
Predator - Argueably Swartzaneggar's best film. Introduces us to the universe's most elusive predator, next to Pedobear. Yeah, I went there.
Serenity - Based off the ever popular Firefly television series; Cowboys in space.
Terminator - Robots from the future time travel to kill all of humanity. Fuck yeah.
Pitch Black - A good idea that came off kinda bland. Universes greatest prisoner escapes on a desert planet inhabited by homicidal aliens. Kind of a groaner, but what do you expect from a Vin Diesel flick?
Star Wars - Ep IV for starters, don't even bother watching 1-3. You'll be disappointed. Any mention of JarJar Binks gets you killed.
Murder on the Moon - Look it up. I've never seen it.
Metropolis - Another cult classic.
How many movies had a giant vagina with eyeballs as a main badguy? That's right, just this one.
Starship Troopers - A book to movie conversion from Heinlein's Starship Troopers. Very very different from the book to the movie, but the movie holds it's own as a cult classic.
Gattacca - Very reminescent of books such as 1984 and Brave New World. Another dystopia flick.
T2: Judgement Day - Robots try to kill us again, but this time go for the kid.
Galaxy Quest - An homage and parody of everything great about the original Star Trek series.
Army of Darkness - Watch this, watch this now! This series is a tribute to the greatest zombie killer of all time, chronicaling his adventures throughout. Hilarity ensues.
The Adventures of Buckaroo Banzai Across the 8th Dimension - Another cult classic that is much easier to watch than describe.
Evolution - Proves that reproduction is usually sticky, wet, slimy, gooey, and generally not very sanitary.
Cube - What happens when a group of ordinary (or semi-ordinary) people get stuck in giant homicidal cube? We get a Canadian film, that's what. Pretty good look into how even normal people will break down in the pursuit of survival.
Akira - Psionic psychopaths will kill us all!
The Abyss - As much of a dousche James Cameron is, he knows how to make good flicks.
Scanners - A Stephen King book to film movie.
Event Horizon - The future of travel through black holes doesn't look too bright.
Moon - Not what I expected from this one. Seeing the previews and having to wait until it was released on DVD (Hell, there weren't even torrents of it out!) gave way to great expectations for the film. In the end, it's twist is completely unexpected but still comes through as a decent Sci fi title.
Stargate - Single handedly responsible for a long run series on the Sci-Fi tv network, multiple spinoffs, and a fanbase more rabid than Stephen King's Cujo.
THX-1138 - Speilburg's college project.
Travel the Universe in style: Get your Space Winnebago today!
Spaceballs - A parody of the great sci-fi flicks of the time. Mel Brooks always delivers!
Blade Runner - There was a strike during the making of this film, so the set designers went nuts during the downtime. A semi-dystopiatic movie and an instant classic. Harrison Ford at his finest.
The Man Who Fell To Earth - Haven't watched it, but it's on the list.
Videodrome - Cult classic
12 Monkeys - One of Terry Gilliam's most memorable and finest films. Bruce Willis along with Brad Pitt really flesh out the characters... also this is the first movie that Bruce Willis ever did where he was killed. He was actually considering not doing the film because at the time all his roles were tough guy characters, so dying wasn't really in his usual script. Ultimately a romance / time travel / dystopian / loony bin flick that's an instant cult classic.
Ice Pirates - Cult Classic
Little Shop of Horrors - One of the very few good musicals. It's an instant classic about romance, plants, and dentistry.
Ghost busters - If you haven't seen this there might be something wrong with you. Bill Murray, Dan Akroyd, Harold Ramis, Sigourney Weaver, Annie Potts, Rick Moranis... Do I really need to continue?
Omega Man - This was on the list.
Equilibrium - If George Orwell (1984) and Aldous Huxley (Brave New World) had to write an action movie, this would be the result. Quite possibly the greatest action/gun romance movie ever done. A must see.
Face/Off - John Travolta battles badguy Nicolas Cage, Travolta becomes Cage, Cage becomes Travolta, Travolta becomes the badguy, Travolta comes after elusive Cage, Cage and Travolta battle it out some more, Cage becomes Travolta again, Travolta becomes Cage again, Cage goes to jail, Travolta lives happily ever after.
A new meme is born
The Fifth Element - Greatest space opera of all time. OF ALL TIME.
Minority Report - In the future your crimes are fortold by 3 little girls that know your going to commit a crime before it happens. Tom Cruise is there to make sure you don't succeed.
Escape from New York - This movie is the basis of the Metal Gear Solid Series. Kurt Russell stars as Snake Plissken. An instant cult classic.
AI - A dsytopian look at the future of robots.
Brazil - Think of Monty Python meets The Office.
Planet of the Apes - "It's a mad house! A MAD HOUSE!"
Eternal Sunshine of the Spotless Mind - Something something something stars Jim Carrey.
Solaris - The future of space travel doesn't look too bright.
District 9 - Aliens come to Earth in a big ship. Big ship just kinda sits there, doing nothing over South Africa. Humans bust into ship, save prawn-like aliens inside. 28 years later South Africa gets fed up with the slums that the prawns have created, so they contract a major weapons dealer to evict them like any decent landlord would.
The head guy in charge of the operation, one Mr. Wikus, comes into contact with some prawn science project and some bad shit starts happening to him. Amazing movie that blew away my expectations. The way that it's shot half mock-u-mentary style, half hollywood film just adds to film along with some amazing acting.
Total Recall - EPIC. One of Swartzaneggar's best, and a damn good sci-fi mindfuck. This is pretty high on the list.
2001: A Space Oddessy - Computers will kill us all, giant obelisks will save us.
Robocop - Cop comes back as a cyborg, kicks everybodies ass and calls it a day.
Judge Dredd - Cop becomes a criminal, but was really a good guy all along. One of the only videogame to movie flicks that didn't actually suck.
A Clockwork Orange - Beatings, rape, prision, and horrific scientific experiments. Sounds like a great Sci-fi flick to me!
Somehow the first pitch to Paramount didn't go over so well
Iron Man - I know that some people are dead set on this movie being crap: I liked it. Even though it doesn't follow the comics, even though it doesn't follow any of the animated series it still stands on it's own. The only thing I had a real problem with that I couldn't live down (as an Iron Man fan) was Tony Stark's alcholism. That was the only thing that this movie was really lacking... and the ending was kinda shakey.
Demolition Man - An action / comedy based around A Brave New World's dystopian outlook starring the Italian Stallion, Syvester Stallone.
Children of Men - In a dystopian future, humanity has become reproductively sterile and obviously chaos ensues. Miraculously, a women becomes pregnant, so it's up to our hero (insert trumpets here) to escort her to super secret sea-based base filled with scientists that will study her and save humanity.
The Running Man - I know, I know... Another Swartzaneggar flick. But who can really blame him? The man starred in a boatload of great action/sci-fi flicks in his day. Running man is a rather creepy prediction of the capibilities of graphics software and the ruthlessness of American entertainment.
Best to stay away from this one if your a horse lover
The Cell - While not a very well executed movie, the concept of being able to delve inside a criminal mind and what lays inside is compelling. The visuals in this one are the real winner here.
Donnie Darko - While this movie is highly contested between utter crap and an instant classic among critics, it does make for a decent Sci-Fi flick. The ending is a mindfuck, the atmosphere created by the characters/plot keeps you watching, and the portrayal of uptight christian suburbia is spot on.
Primer - More to come.
Dune - David Lynch screws with your mind in an epic galatic oddyssy that only really made sense in the 80's... but your going to watch it anyway.
The Jacket - Gulf War Vet is wrongly sent to an insane asylum, where one doctor's experiments either create an alternate reality in the Vet's head or he time travels. Total mindfuck of a movie, plus you get to see Keira Knightly's boobs. Total win win.
Death Race (The original) - There is something just simply satisfying watching a race car plow through an old folks home. A b-movie at best, it stays on this list due to it's camp and pure fun factor.
Charlize Theron's perfomance is... What were we discussing again?
Aeon Flux - While not for everybody, this film really delivered the feeling of the original story from the animated MTV series.
H.R. Giger along with Francis Ford Coppola introduced the world to the Sci-FI Horror genre.
Your next Netflix pick is going to be Alien. Why? Because it is the sole reason the Sci-Fi Horror Genre exists today. Hell, so many movies try and fail to live up to the suspense and drama in this movie. Alien won and STILL wins a plethora of awards today. Not only is this movie timeless, you can watch it again and again without it getting even slightly old. That's how good a horror/sci-fi flick this is.
This list is by no means done.
Even a bathtub/dog/assualt rifle combo can't stop this movie from flopping
I Am Legend - This crappy remake can't stand up to the original. The ending is the real failure of the movie, though. The first half is actually pretty decent.
Kinda forgot about this, huh Fox?
Fox also kinda forgot the part where Magneto rips the Adamantium from Logan's bones. It was a pretty big plot twist... What's that? Oh, no, by all means hire that new writer guy! I'm sure he'll do great on the next movie...
Wolverine: Origins - Possibly the only case where an unfinished workprint copy is better than the finished movie.
You can't argue against this evidence, your honor.
Star Wars: Episode 1 - There is so much wrong with this movie that it damn near killed the franchise. Don't agree? Jar Jar Binks.
We get it already! Your Mr. Smith!
The Matrix Revolutions - We went from a decent action flick (the first one) to a crappy sequel and then... when you thought it couldn't get any worse, they finished (and killed) the series with a third one.
The Lawnmower Man 2 - This was just too horrible to even describe. Stay away... may cause brain damage!
That is a hot mess
Battlefield Earth - If ever there was proof of how badly Scientology fails, this movie is proof. I read the book as a kid and have to say that this movie is just nowhere near close.
Should have worn a condom, Dr. Jones
Indiana Jones and the Crystal Skull - I beleive Southpark has pretty much summed this up already. THEIR RAPING HIM! THEIR RAAAAAPING OUR FRIEND KYLE!
X-Men 3: The Last Stand - I want my money back. No, seriously, I may even sue for pain and suffering here.
There is an amount of story canon that you can disregard when doing a comic to movie conversion. It's pretty hard to wrap up the insanity that is the X-Men universe(s) in three movies, let alone 3. There is also a point where you disregard so much canon that you cease to be writing the same story anymore and you end up writing a fanfic.
That's what X3 and the Wolverine: Origins movies are: Fanfic. And we all know that 99% of fanfic = 100% CRAP.
FYI: Don't cast this women if you expect quality acting and your movie to not suck
Underworld - Single handedly turned vampires into pussys. Made werewolves uncool. Somehow even managed to make half breeds uncool.
Van Helsing - Every movie Kate Beckinsale has a major part in is DOOMED TO SUCK.