Recovering lost user interface

I have lost my user interface and all applications etc. have reverted to unused on my G5 10.3.9 iMac. This happened while I was in Firefox when opening a file just copied from my local networked Leopard MacBook. OS9 applications and preferences do not appear to have been affected and the second user account is unchanged. I have tried booting with the installation disk and repairing the disk but my user account could not be repaired. The name of my user home file has not changed.
Would reinstalling the system software cure the problem? I am concerned that the other user could lose his data and preferences etc. if I reinstall.

It can also happen if the Finder's preference file has been deleted or overwritten. The dialog about opening for the first time occurs when the LaunchServices database has been cleared.
As long as your account is still OK I wouldn't worry too much about this. You will need to re-establish your preferences but otherwise it should be fine. I would also suggest doing the following as a precautionary measure:
Repairing the Hard Drive and Permissions
Boot from your OS X Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Installer menu (Utilities menu for Tiger and Leopard.) After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer. Now restart normally.
If DU reports errors it cannot fix, then you will need Disk Warrior (4.0 for Tiger, and 4.1 for Leopard) and/or TechTool Pro (4.6.1 for Leopard) to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.

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