Ohh, that's a good idea. I roughly do the same, but maybe the thought that something important might be lost would cause me to be more thoughtful about organization on the front end rather than sorting through it after the fact.
Save files to my desktop. When it gets too messy, I throw everything in a folder called "Cleanup". Repeat. When it gets messy again, I rename the Cleanup folder to Cleanup_<date>, then throw that and everything else in a new folder called "Cleanup".
Depends on how hard you wanna go. I dunno about any prebuilt console/control panels, but this guy built a whole A-10 cockpit by himself w/ RasbPI's ;) Pretty neat. I too want a control panel for my apps!