The two things that haven't been mentioned that the C2D MBP includes are: dual layer superdrive and firewire 800. Everything else is sort of "meh" if you ask me. The speed difference is negligible, the 64-bit thing is overstated because the only real advantage it gives you at the moment is the ability to use more memory (3gb versus 2gb real memory). Perhaps it'll make more difference in the future, but that's a long way off really. By that time, both machines will be old. And as far as these so-called problems are concerned -- you shouldn't have any with either computer you buy from the refurb store. If you do, certainly they'll be fixed under warranty.
With that said, the C2D is a better buy for an extra $100.