Empire Strikes Back - For many of the reasons stated earlier in this thread...Hoth, Bespin, Dagobah, first appearance of Yoda and Boba, just the best one overall in my book.
Return of the Jedi - I know many don't care for it, and maybe it is the fact that this was my first "Star Wars experience", seeing it in the theatre when I was almost 7...but I like this movie. I really like watching the Jabba's sequences at the beginning of the film, Speederbike chase was cool (I even like the Ewoks), and the final duel/space battle are both great.
A New Hope - I'm an OT person, so these three are the top three to me, and they are all pretty close. I could watch any of them every day probably and not really get tired of them. I think for me too, ANH would be higher if I had saw it in the theatre too (of course I didn't see the original ESB in theatres either, but anyways). Some of it might be that this is the only one that has been on television a lot too, so I've seen it more. It is a great movie though, and the one that started it all.
Attack of the Clones - To be honest, in 2002 this would have been #2...but that was maybe because of the "newness" of it. When I first saw this in the theatre (several times), I though it was amazing...especially the end part of the film. Every time I have seen it, however, I've cringed at those "Sound of Music" scenes too. I do think Hayden has done a good job though. A good movie, and I do enjoy it, but it mainly ranks here because it just simply isn't the OT...not quite the same, but still good.
Phantom Menace - Again, when I first saw this, even though it was different...I still liked it. Mainly because it was "new" Star Wars I think. I really can't bring myself to watch it anymore, just because I don't stay interested for the most part. The final Obi/Qui Gon/Maul duel is awesome though, and I could watch this portion several times. I still like it, because it is Star Wars, but it is by far my least favorite.
I'm really looking forward to Episode III. From what I have seen and read about the film, it sounds like it will easily be the best of the prequels, and I hope it bridges well into the OT. I think each of the prequels seems better and better, the more things start to look similar to the OT (or characters pop in). First we had the droids, Obi, and Anakin in Episode I (and Jabba, Palpatine too I guess), then we move on to the Fett family/Clones and more OT-looking ships in Episode II, now in Episode III we will see a few more OT characters, or similar looking things (I won't mention them specifically here, because some people are more spoiler sensitive than others...but many know who I'm talking about). I'm looking forward to seeing Ep III though, I hope it satisfies as many fans as possible, and Lucas is able to go out on a high note.