I was considering a barebone cube system but decided not to go for it for various reasons, mainly the fact that it is hard to silence. I'm now looking at a mATX case (Coolermaster 620 to be specific) which seems like a good middleground.
It was a tough call though, since the cube cases look very nice and don't eat up desk space, but since I'm not really confident in my modding ability I decided not to get one.
The new Shuttle barebone systems look nice but from what I've read they are somewhat noisy. For example, the new 220W PSUs have 2x 40mm fans.
VGA cooling is also limited. Most barebone systems have the AGP slot right next to the case cover so it's nearly impossible to passively cool a card without cutting the case.
The new Soltek EQ3401 is probably the quietest of the new P4 based systems. If I remember correctly it also has the AGP slot further in the case so you could fit an Arctic cooling VGA silencer with the cost of the PCI slot.
Check out http://www.sudhian.com
if you haven't already. Lots of info on the site and forums.