Two obvious examples that jump to mind are Monsters and Primer. The guy who did Monsters had experience in VFX prior to making the movie, and applied his skills to make the film look like a professional genre piece while keeping it way under budget (since he could do it himself). If you don't have the time/skills to do VFX yourself, you should take a look at Primer. It's a time travel movie that was made for about $7,000 and won the Grand Jury Prize at Sundance.
The thing about Sci Fi is, it really doesn't HAVE to have all that "glossy/FX" stuff that people associate with it. Consider Primer, Eternal Sunshine of the Spotless Mind, About Time, Upstream Color... You don't really need a big budget and flashy effects to be Sci Fi, you just need a solid (and out there) premise.
This past summer I directed my first feature film for $15,000 (we're currently fundraising on Kickstarter to get another $12,000 for post production), and it was a sci-fi/fantasy film. Our whole budget was equipment rental and catering, with nominal fees going to cast and crew (who were really losing money to work on the project). The trick was that our
idea was high concept and sci-fi, but it didn't require anything more than your average indie film. The premise was: when you go to sleep, another personality wakes up in your place. All that we needed for that execution were talented enough actors to pull of playing two roles, and we were able to find some pretty amazing actors.
Here's the trailer if you're curious about our results:
http://youtu.be/guyyg_ZQt8k
And here's the Kickstarter if you want to find out more (we're still fundraising through December 29th):
http://www.kickstarter.com/projects/jasmerrin/sleepwalkers-feature-film
Good luck!
Jason