Case and cooling
Which came first, the case or the motherboard? The answer to that one is - the choice is yours. The problem with using anything other than a full sized ATX case is that you severely limit your choice of motherboard and may not even find one that is suitable for VTPO work. So it really will pay you to select your motherboard, then find a suitable case to house it.
OK, so let's assume that you've decided on a case/motherboard specification, you now need to decide on the case orientation, which will depend on your preference and where it will be placed in your scheme of things. Do bear in mind that there are a few other considerations with regard to a case for a VTPO PC and that going for a desktop case will greatly limit your choice. It's just 'the way of the world' that (even compact) tower cases are the most supported by popular demand.
The two major considerations at this point are cooling and quietness, and the two tend to go hand-in-hand. Having gone to a lot of trouble to pick other components that are quiet or silent, you now need to look for a case that will not make any noise of it's own and preferably suppress all other internal noise to an absolute minimum. However, it must not do this at the expense of lack of cooling which could be detrimental to the reliability of other components. Your best bet is to look on some specialist websites such as Quiet PC, Silent PC Review and Build Silent PC where you will find a multitude of resources to help with noise reduction.
Preferably either buy a case with a front and rear fan fitted, or buy the bare case and put some extra fans in it. The specialist sites will help here, as they will point to specs for fans that they consider to be quiet whilst maintaining efficiency. Antec in particular make some excellent enclosures and they sell some highly efficient but quiet cooling solutions. Cases with inside padding and adequate ventilation are great choices as they will absorb noise generated from anywhere inside the case.
Having decided upon a range of cases that suit your purpose, narrow the choice down by ensuring that there is enough space inside to mount 'all of the bits in the box'. Pay particular attention to the number of drive bays and do allow for possible later additions. Watch out for cases that have the right number of drive bays but do not allow you to use all of them with the covers on. I bought a case for a VTPO PC that had four bays for hard drives, but it also had a huge 12" fan mounted in one of its sides. The fan worked fine and was very quiet, even at full speed, but unfortunately when the case sides were in place, the fan fouled two of the hard drive bays, making them unusable. To make matters worse, only one of the bays was practically useable as the other was too far away from the motherboard to allow a hard drive to be connected without an extended data cable!
If you want to connect USB and Firewire devices, you'll probably connect the permanent ones to the ports on the motherboard's backplane at the rear of the case. If the PC is going to end up inside a console then it's likely that you'll only need to connect any temporary device (such as a thumb drive) on the same set of ports. If however, you have your PC mounted in a rack or under a desk, facing forwards, then a wise choice would be a case with a USB and/or a Firewire socket mounted on the front of the case. Beware though, there's at least one case out there that looks like the front of a Mercedes Benz (complete with front lights) and has a built in carrying handle. Unfortunately, although it has two very conveniently mounted USB sockets in the top of its handle, the style of socket and the quality of the connecting cables only allows those sockets to be used for USB I. Despite a fully working USB controller being connected to them, those sockets just will not 'crank-up' to USB II speed.
And finally - watch out for some of the cheaper cases that have very sharp internal edges. You can cut yourself very badly on them.