We're talking about two different things here - guilty pleasures, and underrated though worthy movies.
My pick for a guilty pleasure in spite of its detractors is The Hidden - I love it so much I have the special edition!
Great cast headed by Kyle MacLachlin. The Hidden is not groundbreaking by any means, and
of course it's cheesey. But its understated charm, humor and scary bits are nicely done. The sequel sucks, however - avoid it.
Speaking of Kyle M, I would rather watch Dune a thousand times than endure 5 minutes of The Fifth Element or Event Horizon ever again. Yes, Dune's a mess, but it's a glorious mess. If we could only lose the Toto soundtrack in the final third I'd be a happy camper. I like it despite its flaws. If you're gonna fail, fail BIG. The good parts are fabulous and everything is intensely weird. I don't care at all for the mini-series.
More guilty pleasure: I enjoy Enemy Mine. Haters be damned.
While it isn't totally successful, AI is so much more interesting to me than several other more successful Spielberg movies. I find it highly compelling for most of its length. It's an interesting and ambitious film, so I cut the man some slack for the ending. I'd rather see an intersting failure than a successful mediocrity any day.
Not only have I see New Zealand's The Quiet Earth (excellent, underseen movie), I've also seen another interesting Kiwi SF film, The Navigator. Good luck finding it.
More from down under - Weir's The Last Wave. Highly lauded in its day, too little seen nowdays. The Truman Show, also from Weir, is a good try, somewhat hamstrung by its leading man.
A favorite SF of mine is Nic Roeg's The Man Who Fell To Earth. You action fans will hate it BTW. Most of the action takes place in the alien hero's mind. But the movie's an enjoyable ride for the adventurous - just don't expect things all neatly tied up at the end.
I see no one has mentioned a favorite dystopian flick of mine, Code 46, a farily recent movie from director Michael Winterbottom. It's not as brilliant as Children of Men, but it's a fine film in its own right (albeit on a smaller scale). While on this subject, I wonder, does the dystopian A Handmaid's Tale also qualify as SF? I like it a lot, as I like the Margaret Atwood book it's based on. Again, a superb cast (Natasha Richardson, Robert Duvall, Elizabeth McGovern, Faye Dunaway) and a Harold Pinter screenplay directed by Volker Schlondorf.
I'm a huge fan of Dark City - must have seen it 10 times in theaters. Get the director's cut without the voice-over if you haven't seen it before.
I also love Amenobar's moody Abres los ojos - it has subtitles, but do see the original Spanish film and avoid the awful American remake with Tom Cruise.
Y'all must be a fairly young crowd. Silent Running, Soylent Green, the early Planet Of The Apes movies were all very well received back in the day. Brazil, while it never had a huge commercial success, was very highly regarded by critics and fans alike - it's one of the original cult favorites and esteemed by film fans who don't generally care for SF.
If you haven't seen it in theaters, see Moon when it comes out on DVD.
EDIT: For those who haven't yet seen these two classics, be sure to catch Videodrome and The Dead Zone, from director David Cronenberg. And while we're talking thrillers, let me also plug the totally neglected Sf/suspense film Seconds, from John Frankenheimer, starring (I kid you not) Rock Hudson in a very affecting performance.
