Have you made sure to try repairing your drive first? Those files are normally found at the root of the hard drive. Since Darwin doesn't include a Documents folder, there's no way they should be in there.
But I can't see that just moving them by hand will really help. They got into that folder somehow, and that's the real problem you need to address. I've have this sort of thing with severely ****ed-up drives before, so that's my worry -- that all your files will turn out to be corrupt when you move them.