Ok... Superman IS overpowered, no doubt. But along with Kryptonite, he has a weakness to magic. So just use any of the following: The Spectre, Dr. Fate, Dr. Strange, Brother Voodoo, maybe Zatanna. Atlas proved than any guy with magic-based strength can beat Supes, so in theory, the Juggernaut can beat Superman as well.
...Wow, serious nerd moment. And it's only going to continue...
Other contenders:
Thor. He's the God of Thunder.
Silver Surfer. That overpowered Power Cosmic. The only (occasional) good guy to ever use it.
The Hulk. Doubt that? Read World War Hulk. You'll see what I mean.
Dr. Manhatten. Yeah... he probably wins this discussion.
Sodam Yat. Ion has some serious power. I haven't read GL recently, but last I checked he was in the core of a freakin' SUN.
The Sentry. Whiny guy, didn't like him, but he was created to be Marvel's equivilent to Superman, IMO.
There are a bunch more, but I can't think of any.
Edit: Also, Batman. Physically strong? No. But he seems to be able to beat ANY other hero. Which makes me wonder why his villians give him so much trouble.
Dr. Strange. He's the most powerful sorcerer in the Marvel Universe... and there are some pretty powerful sorcerers there.