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.