I'm going to with the movie "Monolith Monsters". It's fairly obscure, B-movie, shot in black and white, which seems to be the kiss of death for so many people today.
I thought it was original, fun, and thoroughly enjoyed it. It's no academy award winner, but as a SF popcorn flick it succeeds on many levels.
I
One of my favourite space-films.I don't remember hearing anybody hate on it but Silent Running never seems to get the respect I think it deserves. Bruce Dern was terrific and the 'droids were delightful. A very moving ending, too.
Brazil - you'll have the song stuck in your head
I remember sitting on the edge of my seat for 'two hours +' that was so brilliant!
Great film! -perhaps it suffers from not having a lot of special effects.If not being well-known counts as being underrated I will go for "The Quiet Earth". I believe it is an excellent movie that suffered because it was made in New Zealand in the mid-eighties.
Phase IV (1974) is both creepy -in that good old fashioned cold war way- and pretty well made for a mid-seventies SciFi -I've always loved it.
The 5'th Element is a very underrated yet highly entertaining modern B-type SciFi comedy IMHO.
Speaking of comedies, Space Truckers is also a favourite of mine.

The character of the crews was laid out pretty well for how little time they were given to be introduced, like the little tidbits with crew interactions suggesting a real familiarity between them all.