I have to go with Season 3. I think that Faith is an excellent character and she carries the season. Faith isn't evil, she's human, she's a complicated character, not just a vamp to dust. The introduction of a human villain, one which has hope for redemption, is what makes this season so great.
I also have to give props to season 6, again, this season deals with some really complicated issues on life and death. Buffy's realtionship with Spike is such a great example. The relationship is complicated. Can Spike truely love anyone, if he doesn't have a soul? The dynamic between Spike and Buffy truely delves into human nature.