OS X Empty Trash is deleting all files on computer
So what is SOUNDS like is there is some serious directory corruption going on with your system.

FIRST make a backup. use disk utility to clone the drive to an image on an external drive, or Carbon Copy Cloner or some such.

Boot your system from the Snow Leopard Install disk and once you select the language to use go to the menu at the top of the screen (Tools?) and select Disk Utility.

Once that is up click on your hard drive and repair it. Then do it again. It could take a while. It is also possible that it won't be able to fix it, but at least you know.

If it won't fix it, my go to Disk repair utility is DiskWarrior. you can buy it online and create a bootable repair disk (note that booting from the DW CD is very slow. 10+ minutes to boot) and let DW do it's thing. And if DW cant repair it you may have to repartition/reformat.

Again, I cant stress enough the importance of backing up everything that you can, even if you have to just drag the files you need from your internal HD to an external one.

Failing all of that, verify your backup is working and then boot from the installer again and delete the old partition, create a new one and format it. Install the O/S from scratch, apply updates and then restore your files.

Not much fun but if you can get your needful files off the computer quite fixable.

Oh just thought of one more thing...

If you go the reformat route and it won't partition or reformat then the drive is probably dying, time to replace it.