Great work! I especially like the V-groove idea. I love doing woodwork, I built some speakers (Audax Home Theatre) a while ago amongst other little projects. I've been thinking about building a desk for some time, much like you there are a lot of good ones but none 'just right'.
Anyway. I was thinking about your cable hole, and possible damage to the edge of the wood when they move/are dragged.
http://cableorganizer.com/desk-grommet/round-desk-grommets.htm
Also, the hidden drawer. Having a gap in the top for air is necessary I feel. Could you cut a slot in the bottom of the drawer? Heat rises, so that should allow air to 'pull through.' Otherwise your airflow will be pretty stagnant.
For convenience sake, I think you'll have to concede on having the iPods/iPhone on the desk. You could no doubt get an old iPod dock from eBay, strip it, and drop the parts into a small cherrywood 'box' (like a thick coaster), if you wanted it to match/be as unobtrusive as possible.
edit: Having USB drives connected slows down boot-up times, btw.
AppleMatt