whoever said Battle LA -really...? Really?!? come on...
Star Wars ESB - perfect combination of effects and story, I've watched it at least 100 times and it gets better every time. The subsequent whoring out of the franchise that started in the 1990s has left me both depressed and speechless.
ok for the rest of this list this is hard for me because there are movies that do a good job of making effects serve the story (Rise of the Planet of the Apes, Source Code) but the effects sort of blend into the background. Then there are movies where the eye candy is just all on display and who really cares whether there's a plot or not (Transformers - all...) So I'm going to toe the line and go down the middle as much as I can.
The Matrix - as ludicrous as the central proposition of this movie is, the film does an amazing job of actually making you believe that the crazy nonsense on screen is all real.
Star Trek - First Contact - I confess this is an indulgence pick but I just love the dynamic of Picard vs the Borg and the action / effects is just terrific. Also, the audio in that film sticks with me for some reason.
Blade Runner - what a fantastic gritty setting for a sci fi film. Honestly, the plot of the movie hasn't aged well for me and a lot of the scenes don't mesh particularly well either but the setting is just so amazing it's hard to care about it's shortcomings.
Terminator 2 - honestly I love the entire franchise and thought T4 was really great but Terminator 2 set a whole new bar for films. Jim Cameron is easily the most ambitious guy in Hollywood and good on him for stepping away from the franchise to do other things like Titanic and Avatar - that guy is great for sci fi and great for film.
As for films I left off that have been popular :
Alien/s franchise - I'm just not a fan - sci fi horror is just not my thing although I do appreciate it - I just dont love it.
Inception is another movie like Rise of the Planet of the Apes that's just a bit too real for me to appreciate it as a sci fi film (yes buildings do fold over in my reality
I see a lot of Serenity out there as well - way too goofy and the payoff on the Summer Glau character wasn't as good as I wanted it to be.