Disclaimer. This is an Applescript which accounts for the primitive interface and slow execution.

What is it and what does it do?
Let me paint a scenario.
So you have a nicely organised desktop. Every icon is in the exact right spot. Good, or so you think. Then you run a demo of a program. It switches the resolution of your screen to 640x480. Actually this is not a problem. But then the program crashes, or unexpectedly quits without restoring your resolution. Now you are in trouble. The icons are crammed tightly into a small space, and they are all in the wrong place. Sigh.

System requirements and installation
You need to have Applescript installed to run this program.
Installation is simple, just put the programs where you can find them.

Operation.
Operation. When your icons on the desktop are in the right position, run Save desktop.
If your icons are moved, run Restore desktop. And they are back where they were when you ran Save desktop.

What's missing.
The program cannot restore positions of popup folders (the folders located at the base of your desktop). This is due to restrictions put upon what you can do with open windows by Apple. A normal window can be resized and positioned but a popup window cannot. A normal window turned into a popup window will forget it's position and size and try to find the first available free slot from the left bottom on the screen.