This strange green rock, made during the destruction of his planet, can be used against Superman. It is eventually lethal to all Kryptonians. Kryptonite radiation first weakens its victim, essentially making them mortal (ie - cancelling out Superman's powers). It then weakens their immune system. After that, they begin to die. The rate of this process depends on the immediacy of the material, as well as the amount. If it were to touch him, death would occur in less than five minutes.
CODE AGAINST KILLING
Due to his experience killing fellow kryptonians, Superman has sworn to never again kill a sentiant being, if there is any other option. This can be seen as a limitation in some situations.
Lois, the love of his life. If anything can be used to throw Clark into a fit of rage, it would be to cause harm to Lois. He has been known to drop important things when she is imperiled. There are obvious limits to this, but this will always make for a good plot device. Sadly, she is dead. However, if one were to ever show up on PIMUX, you can be guarenteed that she would have a built-in protector.
Although this sounds like a comical attempt at a vulnerability, think about it. He will always have to weigh the moral implications of his actions. Period. He works within the law whenever possible. This can be targeted by his enemies.
To all extents and purposes, Clark is not 'vulnerable' to magic. He simply has no defense against it. In other words, he is just as likely to be effected by it as anyone else.