Hi,
One suggestion which may or may not be of use for you: Consider going SMT.
Seriously - I went SMT about 13-14 years ago and haven't looked back since. The boards are so much easier to make, and your parts bins will fit in a small desk drawer. Sure, you'll need through-hole components every now and then, but for the most part - SMT FTW, as the kids say.
If you're curious enough to give it a try, I would suggest getting hold of a few 0805 parts - they are 8/100 of an inch long (2mm) by 5/100 (1,25mm) wide, and 100 resistors should set you back only a few dollars - just to try whether you feel comfortable handling them and soldering them in place. 0805 is - IMHO - a very nice starting point; large enough to be easy to handle, small enough to provide the benefits of SMT.
Also, what I found to be a great help when I was in a similar situation a few years ago, was to make a workbench overlay - basically just a piece of plywood with rubber feet on the bottom side, elevating it an inch or so from the desk. I found it to be of great use whenever I was working on a project, having lots of components, schematics etc, etc all over my desk - when it was time to get some soldering or measurements done, or going over some schematics, I just put the plywood down on top of whatever I was working on (it being cut slightly larger than my ESD mat, so I didn't have to scoop anything away to put it down - I then effectively had twice the desk area. Nice.
Finally, I installed kit which didn't absolutely HAVE to be on the desk below it - think PSUs, signal generator, dummy load, the solder station - I just drilled a few holes in the desk to fit banana and BNC jacks; lots of de-clutterization right there.