The advantage to rackmounting is it's secure and you can service the machine by sliding it in/out on rails mounted to the rack. When you've got more than one machine it starts becoming very tedious to use individual servers resting on shelves. You run into problems with cabling getting caught when you try to move anything. When you use a rackmount setup you can configure cable management arms (or just some added slack) with the wires bundled. This way they won't interfere with other machines when you move a machine to service it. There are lots of rack sizes and options out there. Check with a local computer surplus or recycler. I've got three I picked up relatively cheap that way (around $100-$150 each for a 72U tall rack on wheels).
The other thing to consider is a KVM switch with some nice long keyboard, mouse and video cables. I keep all my gear in an adjacent room, all plugged into a KVM. Then I just run a 35' long bundle of wires from there to my desk. Much, much less annoying than having fans and what not making a racket in the same room. The only downside is I have to get up and walk over there to change an optical disc on the rare times I'd use one. Or to do a hard reset on something, but that's rare.