To me, 2001 is miles beyond any other sci-fi film created - I've watched it at least 20 times and I can't seem to get enough of the set design. It is my favourite film of all time! Contact is another one which I love (both the book and the film...). Twelve Monkeys is another great one (so is the short "La Jetee" it is based on). Gattaca is another great mention. Other than that, there unfortunately haven't been too many good sci-fi films...the recent Moon was pretty good, but I wasn't quite as enthused about it as most other people seem to be. Another film, Sunshine, has quite an awful plot, but it has beautiful cinematography and score so it is still worth watching for those reasons alone. I thought "The Man from Earth" had a decent premise but I found the acting and (especially) the script to be way too cheesy and killed my enjoyment of the film. Primer was a great indie time travel film that took great care in interweaving it's various timelines as best as possible to avoid plotholes, so I give it kudos. Another good one is Cube (obviously the first one, the sequels are pathetic), it is a very fun watch and it is one of the few movies that knows exactly how far to go with its plot.
In terms of the more "fantasy" side of sci-fi, I love Richard Kelly's Donnie Darko, and I even like his follow-up Southland Tales (it is so stupid but so entertaining).
Worst sci fi movies? Well...I don't know if it's the worst of all time, but Mission to Mars is so damn bad it warrants a mention...highlight of the movie being people just walking around on friggin MARS with no space-suit helmets on...all because there are 10 or so small plants they brought with them, which somehow are producing enough oxygen to fill the entire atmosphere of the planet to a comfortable "Earth" level. Gotta love Hollywood :)
There are also some great anime sci-fi films. I absolutely LOVE one called Metropolis, it has a fantastic score and great animation. There's also Akira, of course, which is probably the most famous anime sci-fi, and the animation still looks great to this day. I also watched a pretty good one recently called Memories, which is 3 separate short movies. The first one is my favourite - some people traveling in space come across an abandoned spaceship and go into explore it, only to be haunted by the memories of an opera singer contained within.
If you also count "Dystopian" films as sci-fi, then I recommend Equilibrium and Brazil. They are quite fantastic!