Not sure if these quite count as Sci-Fi, but I'd put up a couple of Ron Perlman's older gems...
Chronos
and
The City of Lost Children

I absolutely loved the 1966 movie adaptatation of Fahrenheit 451 (http://www.imdb.com/title/tt0060390/)
I think it could be classified more like a philosophical reflection than a sci-fi movie, but it's set in a dystopian future so i guess that counts as sci-fi :)

@Panthro - City of lost children is more of a fantasi movie, but a great one nevertheless.
@all
The next gem is from Disney, i only remember seeing it once but i liked it, nover saw it again on tv or for sale. The Black Hole

Well I was talking about the guild navigators in Lynch's Dune movie.

I kinda figured it was Sci-Fi due to the clones and so on.

i Kinda loved split secd with Rudger Hauer (however you say his name) although it was kinda of a horror as well.

Ah, the Black Hole... another one for the Netflix queue... That movie had some of the most memorable robots this side of the Star Wars droids, plus it was a much darker story than your standard Disney film.
Hmm, interesting. After adding The Black Hole to my queue, it popped with a couple recommendations: Tron and The Last Starfighter. These are perfect recommendations to go along with this particular movie, so if you liked either of those films, you will probably also enjoy The Black Hole

Hmmm, I can't really think about any films that are both sci-fi and underdog. But if it's just indie, I think that Primer sort of counts. 12 Monkeys is a great film, thank you Ois for reminding me.

Hmmm, great thread!
I'll write down other titles which are worth mentioning but doesn't seem to appear here.
-The Man From Earth : Not any action, but the actors are outstanding, and the story really interesting.
I can't believe nobody talked about Donnie Darko!
In an other genre of Sci-Fi, Nowhere is really really fucked up and delicious.
Sadly, my memory lacks of any other titles, I'll keep trace of the topic and will post again if I remember more ;D

@aluinie - Split Second is a good movie too. Almost all Rutger Hauer movies are interesting in one way or another, altough most of his movies are underrated.
@cogadh - All of those are great movies. It is good too see that Netflix has a good reference sistem.
@ all
Here goes a couple more underated movie this time with Christopher Lambert, they are and [url=http://www.imdb.com/title/tt0179183/]Fortress 2. The first one makes an interesting approach to an overpopulated earth, corporations and prisons. The second has an interesting twist during the middle but nothing unforeseeble.
Well here goes another classic [url=Soylent Green]Soylent Green[/url] with Charlton Heston, kit has a, shall we say, disturbing ending.

ugh, i hated that movie. the animation style was horrible and the music was nothing to write home about.

Did anyone mention Star Wreck: in the Pirkinning yet?
edit:
Oh and this one on of the greatest sci-fi movies.
And I second (or nth) Primer, spaceballs, They Live, Brazil, Krull, Westworld and Soylent Green

Soylent Green is p-!
Ooh, maybe I shouldn't spoil that, just in case.

I think people unfairly rip on Contact a lot. I personally thought it was quite good and among the best sci-fi movies I have seen.
As for the whole Dune debate I really like it even though it throws out a lot of stuff that the book has. And Dune is my favorite work of science fiction. It's just a fun movie.
Edit: Remembered one more, Alien3. I seriously don't get why people rip on this film. Yes, It's not as good as the first two but I still think it is a good film and has the most interesting setting of the Alien films. Plus Dillion is possibly my favorite character in the series.

Signs wasn't too bad really. They didn't go overboard with the usual aliens-invade-so-now-we-have-to-show-off-their-ships mode. And this was before Mel Gibson started going batshit insane.