My desk is a multi-purpose work space.
Underneath, I have a 2 drawer filing cabinet to the left and a regular tower PC to the right. (IanM is right, size of the PC box is not really a concern.)
On the desk, to the right I have a 19" 12U rack which is straddled between the desk and a storage unit I made. (I could get more space on my desk if I could move that rack further to the right, but the storage unit has a laser printer on it that SWMBO uses, so I only get a third of it.) The rack has an old shelf unit I made sitting on top. Nearly all my accessible TE is located in these (at the moment) and this includes my soldering and hot air stations.
At the back, I have two 27" IPS monitors, leaving the space in front for all manner of work. Wireless keyboard and mouse - so they can be easily moved out of the way at any time.
Above the monitors is a double shelf which contains a variety of bits and pieces which include lighting and a camera for photography, label printer, some commonly used tools and so on. This area is the subject of a complete redesign to allow for placement of some TE - such as my 3478A - to be accessible but out of the way.
I have a direct connect USB extension cable as well as a 4 port USB hub snaking up, coming out from under the rack. The monitors have 3 inputs each - two HDMI and one VGA. They are both connected to the PC as well as one being connected to a microserver. There is a spare HDMI cable connected to one and a spare VGA cable connected to the other. Since dual monitor KVM switches are so expensive (and I don't use that functionality much) I get by with manually switching inputs to the monitors. I did, however, make myself a little USB changeover with a mechanical 4PDT switch in a box with a USB socket for the keyboard+mouse receiver, with two cables. One goes to the main PC and the other is 1.2m that I can plug into another machine.
Behind me to the left is a storage unit for all the common bits and pieces and the other storage unit under the rack, for less frequently accessed stuff.
It is cosy - but I manage.