It was Clyde. He falls asleep in Mr. Garrison's class, which indicates he had a long night. When he meets Cartman on the roof, Cartman says "you're just doing this cause I am, copycat." To which Mysterion replys no, indicating he has been up doing it before. Cartman also says that he knew who Mysterion was and even said it. The only peole that leaves left are Kenny, Kyle, Stan, Craig, and Clyde. When he says Clyde on the roof, Mysterion gets fed up and has to go. Kyle and Mysterion meet, which rules him out. Kenny's family can't afford the suit, and Stan would not be so formal with Kyle. Craig hates adventures, as indicated in the Peru eposode, and he has a nasilly voice that would be hard to change. Mysterion also says he has lived in southpark his whole life, narrowing the spectrum once more.
Mysterion is Clyde.