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And think carefully about that clear top idea. I've used desks with that setup and have found them to be a royal pain. You have to lean way over the desk to see the monitor, which sucks because it's then hard to type.
You can build the computer in the desk if you design the computer portion as the case -- -i.e. don't have a separate case (unless you properly ventillate the desk). What I'd probably do is design a swing out door on the side of the desk. Attach the motherboard to that door. Then mount the drives inside that compartment. Put in a bunch of fans, front and rear, or as an alternative, for the rear fan get a Lasko box fan (they're pretty quiet) and put that in instead.
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