Originally Posted by Stettin
I currently have an enclosed cabinet with two levels. Bottom level is a Yamaha AVR that gets pretty hot. There is less than one inch clearance to the shelf above it. The top shelf has my mini-ITX HTPC. There are two holes at each level in the back. The top level currently has a USB fan that I recently discovered had died. For some reason the fan would run even with the HTPC off. Even so, it didn't cool off the cabinet that much, so I've resorted to cracking the door open for some more air flow when the AVR and HTPC are on..........]
Not sure I have any earth-shattering advice, but here are a few rambling thoughts:
To blow air efficiently out of the enclosure you need to allow an equal volume of air into the space - this is why cracking your doors open helps lower the overall temps. One of the ways to do this in your situation is to drill a couple of holes in the base (assuming that the lowest shelf is not above a sealed space) and in the intermediate shelf - at a minimum this allows the air to rise passively as it gets warmed. Another approach might be to cut an additional pair of holes in the right hand side of the back [maybe even constructing a rectangular 'periscope-like' plenum behind the holes that allows cooler air to be drawn in from floor level] to provide unrestricted ingress of the coolest air in the room into the cabinet.
Most PCs suck air in from the front and blow it out of the rear of the case - if this is true for you, I'd make sure that I had a hole lined up with the rear exhaust port/grill to ensure that the hot air stood the best chance of actually being ejected from the cabinet. I'd be concerned that the current location of your top fan means that it is fighting with the fan in the HTPC - compromising getting airflow through the PC's enclosure as the designer intended. For the HTPC shelf, if this were my set up I'd again probably locate a hole a the far right side and use a fan and the plenum concept to suck cooler air into the upper void, I'd then construct some form of cowling immediately behind the HTPCs exhaust opening (making it as airtight as possible to minimize leakage back into the cabinet) and cut a hole in the cabinet immediately behind this - assuming the PC's fan is adequate, there probably is no need to use a second fan to blow air out of the top shelf space. The limited clearance in front of the HTPC will obviously impede the efficient flow of air into the case, but if you're getting cooler air into that top space you are in a much better place than before.
In terms of swapping the two units, the general rule of thumb is to locate the devices in descending order of heat output - putting the one that generates the most heat at the top. I suspect that the HTPC probably emits more heat than your AVR, so I think you're good as is. It's not clear if there is a gap behind the middle shelf, but you obviously still need to deal with the AVR's thermal output. I know that vertically centering your holes is the right thing to do from an aesthetic point of view, but you need to consider the airflow path through the AVR - with your proposed config there's a possibility you could be trying to blow air into the cabinet very near to where the AVR is trying to exhaust it, I can't tell. Again, you need a similar sized hole for air to enter the enclosure as you have for exhausting it - don't confuse stirring up the air with actually pulling cool air in, getting it to pass appropriately through the components, and exhausting it properly from the cabinet
If you can face it, the doc linked to by Geenowalker is a probably the definitive treatise on 'thermal heat management' - it gives you the fundamental tenets of how best to avoid frying your gear.
Hope something here helps!