Season Three by a mile. It was the only year I truly enjoyed the show. The opening arc switching between realities was the high point of the series, and the second half was almost as good. S1-2 was just chock full of standalone episodes I did not care at all for. There were only a handful of good episodes. I actually stopped watching mid-way through S2. Season Four was, enh. I really REALLY did not like the fact that the continuity rebooted, we weren't with the same characters anymore, and the mirror universe was gone. Season Five wasn't very good either. I commend them for moving into a Observer-ruled future, BUT every episode was just about going after some Macguffin and I just didn't care.
^^ What did you like about S1? I found it pretty uninteresting until they revealed the alternate reality, but that was only a couple episodes. For the most part it was an uninspiring X-Files "homage" that didn't seem to be going anywhere, and I got really sick of them keeping around the Human Target guy.
My order... 3 2 1 4 5 I wish the show ended with season 4, and just replace the last 30 seconds with something else.
Season 3 was my favorite. Season 4 started off slowly but picked up steam in the latter half. Season five has been almost as good as 3. I liked Fringe from the start. Loved the Heinlien-esque lineup of old man, young guy, young girl. Loved Walter. This character helped sustain the show for me through some of the more mundane standalones. I also appreciated the fact that unlike the X-Files, Fringe was about the real physical world rather than the paranormal. Though I recognized they were going for an X-Files dynamic, I thought it was nice that they drew the line somewhere.
Without question...Season 3! I enjoyed season 1 and Season 2 was fun, but season 3 was the highpoint of the series. I considered the entire parallel universe plot to be at the core of the series and season 3 was where it reached its peak. I loved the flip flopping between the Red and Blue universes...and frankly it was always fun to find the little easter egg details that showed the differences between universes. Plus I found the first alternate future far more interesting than the one we ended up spending time undoing.
That was fun. I think my favorite was the movie theater marquee showing Back to The Future, with Eric Stoltz.