Well, as fellow geeks I am pleased to see a wide variety of sci-fi in there. There were many films that I had not thought of in years, i.e. Short Circuit. (Thanks for that.)
I was more than please to see Stanley Kubrick's best works mentioned: Clockwork Orange and 2001: A Space Odessey. 2 all time greats.
My top 5 are:
2001: A Space Odessey
Flash Gordon (1980) Which has recently come out on DVD, not that I didn't have a pirated copy on VHS, but still
Airplane! (The penultimate in literal humor. Can't go wrong.)
Monty Python and the Holy Grail (Suprisingly, the least obscene, but I think by far their best movie.)
Unbreakable (M. Night Shayliman(sp? sorry) knows his comic books.)
Very honerable mentions:
Strange Brew - ya, hey there! Take off, eh?
Cowboy Bebob: The Movie (A great way to suck others in. "I love a woman that can kick my ass" is movie magic!)
Sky Captain and the World of Tomorrow - I know Gweneth Paltrow look absolutely ancient in re-colorized b/w, but that movie was absoluetely brilliant, like Amy Winehouse (If you were ever a Shirley Bassey fan, check her out.)
The Shining - Once again Stanley gets it. Not all Stanley Kubrick is brilliant, but this is worth mentioning.
Serenity - Previously mentioned, and I strongly agree
12 Monkeys - I am surprised that this wasn't mentioned at all! I am sorry, but you have to have a time travel movie in your collection to even consider yourself a "geek". Planet of the Apes is more than acceptable to fit that bill, not my cup of tea, but definately a worthwhile mention.
Alien - only the first one. Again, I see no mention! I am a little disappointed.
Lord of the Rings - Come on! This is another penultimate Geek film series! No mentions? I am saddened.
Stupid Sexy Flanders series - Previously mentioned. I am glad.
Pirates of the Carribean series - Ditto
A Christmas Story - A geek holiday CLASSIC!! Again, no mention. What kind of geeks are you all???
Top Secret - Little known, glad to see it recognized previously!
Highlander - (There can be only one, the first one)I recently went back to this movie and realized how bad it really was. I will NEVER part with it in my collection. I am a GEEK and proud of it, damn it!
Kevin Smith series (Clerks, etc.) - Glad to see the hat tip to this series!
Office Space - I think, now that I give it a little thought, this is the ultimate "Cross-over" movie between Geeks and the rest of society. Again, no mention. What kind of Geeks are out here?
Naked Gun - Pick one. If you loved Airplane! I recommend the first one, but any of them will do.
Crouching Tiger, Hidden Dragon - If you won't venture into international film, pick this up. And, as with any international film, read the sub titles, it is a much better movie
Akira - You have to have a true Anime movie in your collection. I would recommend this above all others.

Personal runner ups: (The others I am going to "force" on you. I know, I am an arrogant S.O.B.) These are personal recommendations:
The Prophecy - Only the first one. I love religous movies!
The Body - An interesting conundrum...
Kill Bill (1&2) - This is one movie. Personal recommendation
The League of Extraordinary Gentlemen - This is best viewed drunk, which is where it holds a special place with me. I first saw this at the "Brew and View" in the city of Chicago.
Contact - May the Universe that he loved so well look after him. Thanks, Carl. For everything.
Hudson Hawk - "David Addison's" one and only movie that I love so much
Aladdin - I think that you should have at least one Disney movie in you collection. This is my pick. Robin Williams. Can't go wrong.
Dead Poets Society - Speaking of Robin Williams... This movie put him on the Academy's radar.
The Birdcage - Damn funny. And it isn't Robin that makes it so damn funny.
Steel Magnolias - I am sorry Olivia Dukakis and Shirley McClaine are fall over funny (Not to mention, having these 2 movies in your collection shows your "sensitive" side, if you are straight, and your willingness to laugh at yourself (a bit) if you are not. These are "get laid" movies, regardless of preference. Use that to your own evil and diabolical ends.)

I know this is a movies link, but here is my short list (that I own) of TV series:
Firefly
The Family Guy
Cowboy Bebob
Samuri Champloo
Robotech
Quantum Leap (I don't own it, but I am trying!)