Mine is almost the same as Alina. I flip-flop back and forth between liking S2 or S3 a little better though. I think S2 has more of my favorite eps, while S3 has more long-term arcs that I like.
Right now, my list is -
S2, just for the eps that are my true favorites (Bracebridge, ICGS, Run Away, Little Boy, and others)
S3, for more Jess and less Dean, Lane and the band, Trix. Hate the Francie stuff though.
S1, again for the favorite eps (Rory's Dance, F&S, RBP, Cinnamon's Wake, Double Date, Concert Interruptus, etc)
S4, I enjoyed Jason (just wish he wasn't there to date Lorelai) and it was fun watching Rory and Paris get used to college life. Plus, it has Tanna.
S5, because it's not S6 or S7
S7
S6