I was born in 1951, the year science fiction made its big comeback, so I've always felt a special bond for this genre. My list is going to be extremely long because I have that many favorites. The majority of these I have seen 100+ times and will continue watching them as often as I can.
Foes
Kronos
Predator
Stargate
Dark City
Moontrap
Pitch Black
X-Men trilogy
Lifepod (1981)
Alien tetralogy
Donovan's Brain
Phantasm series
Forbidden Planet
This Island Earth
Metropolis (1927)
Fantastic Voyage
Monolith Monsters
High Plains Invaders
When Worlds Collide
The Last Starfighter
Chronicles of Riddick
The Terminator & T2
V (original miniseries)
The Angry Red Planet
First Men in the Moon
20 Million Miles to Earth
Battle Beyond the Stars
Robinson Crusoe on Mars
The Man with Two Brains
The Colossus of New York
It Came from Outer Space
The Whisperer in Darkness
E.T.: The Extra-Terrestrial
Earth vs. the Flying Saucers
The Incredible Shrinking Man
Caltiki: The Immortal Monster
The Andromeda Strain (1971)
The Lost Skeleton of Cadavra
The Thing from Another World
War of the Worlds (1953 & 2005)
Close Encounters of the Third Kind
Something Is Out There (miniseries)
The Day the Earth Stood Still (1951)
Spider-Man 1-3 but NOT the "reboot"!
I Married a Monster from Outer Space
It (miniseries) ~ After all, It is an alien!
Sky Captain and the World of Tomorrow
Invasion of the Body Snatchers (1956 & 1978)
The Asphyx ~ falls into that SF/horror category
Sherlock Holmes (2010) ~ I love this steampunk tale!
Five Million Years to Earth aka Quatermass and the Pit ~ I also like the other Quatermass movies.
Star Wars saga ~ ALL OF IT! I can't believe the bratty public pouting after George Lucas gives us these works! I was in my mid-20s when the phenomenon began, and I for one still appreciate all that he has done!
Star Trek saga with original cast ~ I don't mind a couple of the others that follow. However, I despise, detest, loathe and abhor Abrams' travesty! Shame on him! Where was the Roddenberry estate that this was allowed?!
Jurassic Park trilogy ~ Here's an instance in which the ridiculously fickle public turns its back on amazing filmmaking. There are flaws, but these are fantastic adventures with wonderful effects~CGI put to good use for a change.
John Carter ~ Too bad that so many people lack knowledge of Edgar Rice Burroughs or they would have known that he was one of those who led the way for other science fiction writers to come. Disney did a remarkable, commendable job! Unfortunately, they released this to a mostly uneducated public when it came to classic SF literature. I hope that it ultimately makes enough money for there to be a sequel. Meanwhile, millions are thrown away on the trash heap of "Transformers", a reboot of Spider-Man, and Abrams' slaughter of pretty much everything basic to "Star Trek".
I love giant monster movies, which generally involve radiation or The Bomb: Them!, The Beast from 20,000 Fathoms (which inspired Godzilla: King of the Monsters), The Deadly Mantis, Tarantula, It Came from Beneath the Sea, The Giant Behemoth, Deep Rising (perhaps more horror than sci fi), Godzilla (1998), and The Host (fantastic creature in one of the few modern-day creature features).
Ridley Scott might have mentioned "This Island Earth" in connection with "Alien", but the two bear no resemblance at all. However, two other movies had to have inspired "Alien": "It! The Terror From Beyond Space" and "Planet of the Vampires" aka "Demon Planet". The latter even has a gigantic, skeletal "space jockey" in a crashed ship on a fogbound alien planet to which ships are drawn by a distress signal. "It!" has an alien sneaking aboard a spaceship and killing off the crew, the basic plot of "Alien". Mario Bava's "Demon Planet" definitely is worth checking out! "It!" is extremely low-budget, so don't expect a lot except some entertainment.
I know I must be forgetting some favorites, but I'll stop there. Hey! I'm an old lady! I have scads of movies I love=}
EDIT: In "Planet of the Vampires", this part is when they've found the giant crashed ship and enter. You'll note the skeleton, which, moments before, topples when they touch it.
http://www.youtube.com/watch?v=jLM8YF7EaVE
The prior bit is on Part 5, of course.