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.