Having had some time to sleep on it, here's what I think. Can't match tekumseh though that was deep....
S1 = S4 > S2 > S6 > S3 > S5
Season 5....the bottom line for me is that in my inevitable rewatch, I know that this is going to be the hardest season to get through. I still love it of course because this show has always been entertaining, but I really don't like the time travel aspect that much. Just ended up feeling like a wasted opportunity. Also, I think that S5 has the worst season finale which doesn't help. I don't really feel like there was anything necessarily "iconic" about this season. No images really stick in my mind, no moments that really stick out as being above and beyond anything else, just feels like the most "bland" season to me.
Season 3 had an amazing final run, but the beginning and middle half of the season really drags it down for me. Outside of Juliet, I was not a fan of the Cage/Hydra island stuff. Those last 4 or 5 episodes are brilliant though. And it has one of the better finale's (Hell, the on Island stuff in the S3 finale is actually a bit better than the on Island stuff in The End). I really enjoyed everything with Alex and Rousseau as well. Above all else, I'll remember this as the last season in which Ben and The Others were completely in control and menacing. One thing the later seasons missed that I loved about the earlier ones.
Season 6 had some great highs, also had some lows for me. I think this season may have really benefited if they had rearranged some of the episodes around. Honestly, in retrospect, I feel as though the season as a whole as well as fans reactions to it would have benefited had they aired Across the Sea as the premier (As crazy as that may sound). I think the big beef people have with the show right now is that they aired this episode towards the end, making it seem as though they were either 1) Setting something up for the finale or 2) Answering everything so that they wouldn't have to in the finale. I feel like it would have been better off really early in the season. When I rewatch the season, I'll probably watch this episode first. Be it as it may, I feel that The End may be the best season finale.
Season 2....sort of a guilty pleasure for me I guess. Like I've said a few times through the thread, I just really liked the "weirdness" of this season. I pretty much liked everything that dealt with the Hatch and the Others. The season premier is probably my favorite premier in the shows history. Introduction of Desmond. Introduction of Ben. Orientation films. One of the better middle of the season "what the hell" moments in The Other 48 Days. Tons of great friction in this season. Between Jack/Locke/Sawyer/Eko/Ana Lucia/Kate/Sayid...just felt like a lot of drama underneath everything that was going on and I loved that. If this season had been condensed down to less episodes like the final 3 seasons, it would be the best season. What held it down was all the filler they had to throw in.
Season 4....the most tightly wound season. This season ranks so high for me personally because it feels like the most "shot to air" season...not sure if that makes sense. It just seems like this season, more than any other season, was well thought out before hand, and executed to perfection, making it the most consistent season, with little filler. I really liked everything that happened on the freighter, great casting, and was a nice change of setting for an on island story. Also, the flashes in this season are pretty much unmatched for me, Oceanic 6 storyline really worked out (And was helped by non-06 flashes also being great). Can't wait to give this a rewatch.
Season 1, tied for first, but completely different than season 4. Looking back, this season probably could fit anywhere on the list because it's sooo different from any other season, it almost deserves a separate tier, but I guess that's what makes it so perfect. This is the only season where people compare episodes from later seasons to, "That felt like a season 1 episode"...always in a good way. I could never get enough of those "nightly speeches" from Jack and/or Locke. The island interior was sooooo scary in this season...the show actually had a good bit of horror conventions in the beginning. The "hook" of this season of course was watching these character get to know and love/hate each other. Beginning of the love triangle (Before it was annoying as shit), beginning of Jins fantastic character arc, set the stage for faith versus science, set the stage for Locke versus Jack, just so much going on under the regular plot this season.