ArcMap 9.3 Toolbox Empty Issue
This is from the ESRI support forum thread http://forums.esri.com/Thread.asp?c=93&f=1727&t=276619. The registry can be accessed by going to Start/Run and typing regedit in the command line box.
1. Close ArcCatalog or ArcMap
2. Rename the ESRI folder in your registry
HKEY_CURRENT_USER/Software/ESRI
to
HKEY_CURRENT_USER/Software/ESRI_OLD
3. Restart ArcCatalog or ArcMap, this will generate a new folder called ESRI in the same place in the registry.
Another suggestion on the ESRI support site said to delete the normal.mxt for the particular user logging in to the computer. ArcGIS will regenerate the normal.mxt from it's default file. The one to delete can usually be found in C:\Documents and Settings\<user>\Application Data\ESRI\ArcMap\Templates.
Lastly, rename ArcToolbox.dat in C:\Documents and Settings\<user>\Application Data\ESRI\ArcToolbox. Change the .dat to .bak and ArcGIS will create a new .dat file.
Note: If these do not work, I would try a repair on the install and try again.