Season 5. The best season of Lost, by far. One of the best seasons of TV, out of all my favorite shows. This is the season in which Lost peaked.
Season 5 - Favorites
[5.10] He's Our You
[5.11] Whatever Happened, Happened
[5.13] Some Like It Hoth
[5.14] The Variable
[5.15] Follow the Leader
[5.16] The Incident (Part 1)
[5.17] The Incident (Part 2)
Season 5 - Honorable Mentions
[5.01] Because You Left
[5.02] The Lie
[5.04] The Little Prince
[5.05] This Place Is Death
[5.07] The Life and Death of Jeremy Bentham
Yes, that's no mistake. I count every episode of season 5 as either a favorite or an honorable mention except [5.12] "Dead Is Dead." Even that episode was still decent. The season is just that good.
Basically, season 5 is the time travel season. On the island, Locke, Sawyer, Juliet, Jin, Miles, Daniel Faraday, and Charlotte are bouncing around in time. According to Lostpedia, they experienced at least 14 time flashes. In those flashes, one or more people each got to witness the birth of Aaron, the washing ashore of Rousseau's science group on the island, the presence of an atom bomb on the island in the 1950s, and the Tawaret statue being intact on the island in an earlier century.
I love the time flashes. The only thing better is when the time flashes stop, and the survivors join the Dharma Initiative in 1974. It was great seeing James (hard to still call him Sawyer at this point) taking up a respected leadership position and even better to see him in a relationship with Juliet. It's funny; after three seasons of developing the Jack/Kate/Sawyer love triangle (and, maybe a few months of Juliet just barely making it a "love trapezoid"), all it took was a few scenes of seeing James and Juliet together for their relationship to be just as believable as Sun and Jin's or Desmond and Penny's.
When Jack, Kate, Hurley, and Sayid time flash back to 1977, after the other Losties have lived comfortably in the Dharma Initiative for three years, there's this horrible sense that fun time is over. The game is back on. While the final hours of season 5 aren't as action-packed as season 4, it's even better because of the tension between characters, the philosophical aspect of fate vs. free will, the nostalgia of seeing the Swan station being built, and the big question as to whether the group could -- or should -- try to change their pasts. And, the final moments of the episode are the most jaw-dropping and gut-wrenching of the entire series, and again, it's because of the believability of the James/Juliet relationship and how much Juliet was my favorite character.
Other highlights of the season include: Hurley trying to write The Empire Strikes Back for George Lucas, finding Rose and Bernard (with Vincent) who are hiding from both Dharma and the Others because they have "retired," Miles getting to interact with his dad and finding out he wasn't so bad after all, the horror of knowing that Eloise Hawking killed her own son, getting to see Hurley drive a fully intact Dharma van, and Hurley asking Miles questions about time travel that some of the audience were probably wondering too.