Personally, I have always found Season 3 to be the weakest of the entire series, however, it continues to stand as an absolutely incredible season of television, that far surpasses most other television.
This season, we are basically introduced more closely to the Others, and it was one of the most compelling stories that was told in Lost.
As perfect as it was, however, it just didn't know what was coming after it...and, Season 4,5, and 6, were the three finest seasons of television I've ever witnessed!