Silent running was one of those rare flicks that walks a nice line between deep thought premises and entertaining story and expansive special effects (as opposed to intimate films which deserve their own category).
Chief on my list is Blade Runner. ghost in the machine (1995) Clockwork Orange
Silent running is good but it doesn't hold up with time very well.
powerful intimate films:
moon, ex machina, the man from earth, primer
other low budget sci-fi with high entertainment value:
The 13th floor (overshadowed by being released near the Matrix)
John dies at the end. (really awful but in a wonderful awful sort of way like Bill and Ted's excellent adventure was goofy good).
Time Lapse. Some uneven acting but a thrilling story
Films that succeed by sheer force of will rather than being perfect and must be admired for this tour de force:
Avatar, Alien, Star Wars.