I've been thinking about that also...I wanted to build a wooden case not just for the challenge, but also because I felt it was more expressive and of course more unique than metal. With that said, I have not actually done anything yet to build one. My thought process might be of help to you though.
1. Buy a well constructed case (probably not too expensive because you only need a frame)
2. Depending on how much you want to cover the case in wood is up to you:
http://www.coolcomputercases.com/wooden-computer-case.htm
or
http://www.directron.com/contest1win.html (third place)
or
What I wanted to do was have a less structured case with a flat bottom and the sides to have contors which were natural to the wood. The case would be smooth and natural looking but not in bad taste.
Buy the kind of wood you like - ebay has a great variety. I personally wanted to make a teak case, but that wood is too expensive. I would go for any wood you find which you like. Just make sure that when you buy the wood that it is dried wood. Wood which isn't 100% dried and is exposed to 0% humidity and hot temperatures will warp - ruin the case.
3. There are all sorts of shapes you can get. Try to get something that will fit well on your case frame. Maybe even buy two kinds of wood and make a pattern - be creative. Don't get a "busy looking" wood and contrast it with a dull wood though. Wood with highlights or a flame and a nice grain will look best.
4. Be careful of the wood while cutting/shaping it. Wood can be surprizingly inconsistant and decieving (but isn't that what makes wood beautiful?). Go slowly because if you mess up, often the repair isn't as nice looking. Often one can take a piece of scrap wood with a similar grain and glue it into the hole that you made by mistake. It is hard - very hard to repair a mistake, so don't make one in the first place.
5. Be creative. Mix metal and wood or mix wood and art. Whatever you want to do - just do it carefully.
Be prepared to spend a LONG time on making this case if you want it to be a nice looking piece in your house
