After watching all of the seasons in the past few days straight through, I noticed really high and somewhat low points.
The worst is probably season two. I don't know why, it just didn't seem as funny.
The best is probably between 4, 8 and 10. 10 had Cartoon Wars and Go God Go. Those two double episodes alone are pretty amazing. Season eight has the Woodland Critters, Douche And Turd, You Got F'd in The A and a bunch of other kickass episodes. They're all awesome. Besides "Pip" and "Fat Camp", season 4 packs a good punch overall.
I think 6 is a good season as well. Asspen is my favorite episode. I can't say what the best season is, though, without watching the episodes over. Which I won't.