ok
I can help with the easy fix at least.

To run the automatic system file check ("Safe Boot") ,
-shutdown your machine, wait ~3 minutes, and restart. As soon as you hear the start-up tone,
-hold down the shift key (you can let go once you see the grey spinning cog). After quite a bit longer than a usual startup, the splashscreen will show "Safe Boot"

Let it continue, and with luck, your desktop and folders willl be back to normal.

If not, please post your machine specs. Just go to the Apple menu -> About this Mac to get
OS X Version (10.3.8)
Processor (700 MHz G3)
Memory (384 MB)

Then click once on the hard drive and use command-i to get the used/free numbers

Available (3.1 GB)
Used (24.83 GB).