Season Six is, overall, the most interesting season. Just think what it offers:
1. No Angel at all. This is a huge mark on the plus side.
2. Minimal Riley.
3. Buffy finally fucking Spike.
4. The Musical Episode.
5. Dawn actually fighting.
6. Dark Willow. By far the biggest mark on the plus side.
7. The alternate vengeance demon.
8. Xander doing something interesting as a character. Yes, leaving her at the alter is a douche move but at least he's not just comic relief.
9. New Improved Giles - Now With Magic Powers!
10. The really, really interesting way that the attempted sexual assault plays out. Consider how Buffy still feels safe leaving Dawn with Spike afterward. Joss handles a really touchy subject really well and gets into how complex everyone's reaction to the event is.
Yes earlier seasons have better individual episodes and I'll always love Glory, but taken as a whole Season Six has more to offer than any other individual season.