Ok, so I think we'll refinish the hardwood.

Dh wants to go with a natural carpet in the den - I'm not sure we could get the original wood floor matched in the den without spending a bunch of money. So, he thought we could experiment with wool carpet in there. I'm not completely sure, but it sounds better than synthetic carpetting. I do love the idea of natural fiber area rugs in the rooms where we want them.
Silly decorating question: If the house is all travertine tile or hardwood flooring, would it look silly for the den (which is accessable from the tiled kitchen or the wood floored living room) to be something like cork? For some reason, it seems like it'd look fine carpetted, and I don't want it tiled, but I'm not sure about what to do in that room. Ideas?