Season ranking time...
Season 1 is one of the best seasons on television ever, with maybe one of the best pilots ever. A great air of mystery surrounds the whole thing, and you're constantly saying "What the...?" (in a good way)
Season 2 can get a little too bogged down, a lot of new characters are introduced, and the season becomes mostly about the Hatch. Some stellar episodes, though, most notably the Tailies flashback episode. Things pick up towards the end when Ben shows up and Michael starts flipping out.
Season 3 told a great cohesive story, despite all the complaining from the fans. A couple throwaway episodes (Niki and Paulo), and some completely pointless flashbacks (Jacks tattoos), but the good outweighs the bad. We start to get a feel that the survivors of 815 might be just as capable of murder as the Others. A lot of nice themes are presented. Terrific finale.