Of the three early seasons, I liked Season 3 the most.
Season One had awesome episodes like "Mr. Hankey, the Christmas Poo" and "Pinkeye", but I found some episodes like "Damien" to be slightly boring in some parts.
Season Two was the longest season of South Park and one of my least favorite because of episodes like "Chef's Salty Chocolate Balls" and "Roger Ebert Should Lay Off the Fatty Foods", but "Ike's Wee Wee" and "Summer Sucks" were some of my favorite that season.
I absolutely love Season 3 because it's the last to have the original intro and because of Heidi's first appearance. I loved the episodes "Rainforest Schmainforest", "Tweek vs. Craig", "Sexual Harassment Panda", "Chinpokomon", "Hooked on Monkey Fonics", "The Red Badge of Gayness", and "Mr. Hankey's Christmas Classics". Some episodes I felt got a little boring were "Korn's Groovy Pirate Mystery" and "Starvin' Marvin In Space".
I think Season Three took what Season One did right and improved on most of it, making more enjoyable episodes that still hold up pretty well today.