I must agree with all the above responses....this question is too hard! I can't narrow my favorite sci-fi movies/series down by that much!
Incidentally, if my avatar doesn't lend a clue as to one movie that would certainly be on my list:
Serenity (under the assumption, as mentioned above, that one has the back-story from Firefly)
Close Encounters of The Third Kind
Dune (SciFi miniseries, if it can be counted as a movie 'series')
Not necessarily in that order and only marginally more favored than many others in my collection...
Edited by appophylite - 9/4/10 at 5:08am