+1 for the Floor... although what I've done is grabbed a bit of wood cut to just slightly larger than the footprint of the tower, then got some of these big flat-dome-shaped plastic furniture feet and attached them to it. Keeps it just slightly raised from the floor to help with dust (but really dust filters take care of most of that anyway as long as you remember to clean them now and then) and makes it easy to slide out if I need to get at the inside...
Also grab a big set of the largest bulldog clips you can find, and some large metal washers - if you screw one side of the bulldog clip handles into the desk (using the washer to hold it in place) they are an amazingly good way to manage the cables