For me Season 4 was the best season, especially seeing that the writers were under pressure due to the strike! It combined the right level of heartfelt emotion and island mythology! The flashforward literary device worked perfectly, allowing us to capture the many differences between the islanders and their post-rescue lives!! The addition of the freighter folk proved to be surprisingly clever, as Charles Widmore's interest in the island sparked a wave of theories regarding the universal significance of the Island itself. Finally, the series finale "There's No Place Like Home" is one of the finest episodes ever produced on television. The musical score was beautiful, and while we knew what the eventual outcome would be (the Oceanic Six leaving the Island) nothing could prepare us for the twists and turns along the way. This episode featured a lot of Ben/Locke interactions, a pairing that leaves me even more intrigued with every scene I watched. Season 1 was a close second, purely because of the excellent use of flashback as a means of juxtaposing the on-island events with past incidents in a character's lifetime.
I don't want to talk to much about what I think was the worst season, because Darlton have delivered five fantastic seasons of drama, suspense, romance and mystery. I feel most fans will agree that Season 3 lacked the oomph needed to answer the litany of questions that were posed in Season 2. Of course this was not helped by the mid-season break, but the time that Jack, Kate and Sawyer spent in the Others' camp was one of the most frustrating aspects of this season for me. This, combined with the somewhat random addition of Nikki and Paulo to the cast, left an unpleasant bitterness in the mouths of the show's loyal fans. Luckily, the second half of Season 3 was very impressive, mainly due to the enormous influence that Penny Widmore (seemingly) had on the potential rescue of the castaways. "The Man Behind the Curtain" answered many of our questions rather satisfyingly, and Charlie's death was a noble act of self-sacrifice.
What do others think? Feel free to disagree.