I love Season 1. It's probably my least favorite season, but only because of how short it is. Personally, I love how almost innocent the season seems compared to the later ones, plus there is alot of great character moments sprinkled throughout. "Prophecy Girl" alone is worth it.
Personally I think Season 4 is the most underrated season. Yes it has "Beer Bad" and "Where The Wild Things Are," but there is still so much great stuff this season. Episodes such as "Hush," "Restless," "Who Are You?," "Something Blue," "Primeval," "New Moon Rising," and "Wild At Heart" more than make up for the occasional misguided episode.