I have had this problem as well. I actually had it start with leopard & then continue to get worse on Snow leopard. I have a friend who is a Mac genius and he suggested a few standard things that I should try. he thought it could be bad RAM or a failing hard drive. After booting from an external & still having the same issues, and the RAM I have being brand new, he’s thinking a fan might have stopped running and the graphics chip might have toasted itself. He suggested running a hardware test now (if I can find the disc). We’ll see what happens next.
But you are sadly not alone.