At one time, I voted Superman on this question (and this is at least the third time we've covered this ground...
...always fun though!). But since then, I've changed my mind and gone with Thor.
Superman's vulnerability to magic is one of the main reasons, sure. But there's also something to the fact--at least for me--that Thor is a God, and Superman, for all his power, is just a guy from another planet. Granted, there's a philosophical question to be raised here--how is a very powerful guy from Krypton different from a very powerful guy from Asgard? But still, to me, there's a difference. Thor's all about magic--divine magic, maybe, but there's never been a separation between the arcane and the divine that I know of in terms of Supes' vulnerability.
It'd be a very tough fight, I have no doubt. But I do think that Thor would take it.
And I can't tell you how much I dislike Superman's "in my world, the dials go up to eleven!" line. I mean, come on...does Superman need to quote Spinal Tap? Seriously? That's a Spidey-line, at best.