Here is a batch process that we use in Deployment Solution to modify the registry (HKEY_CURRENT_USER) for each user on a system without logging them in.
The batch reads in each folder under "C:\documents and settings" then loads the ntuser.dat file using the reg.exe command line. Makes the modifications, in this case a couple of settings to IE. Then it unloads the hive. It does however fail on the user ID that is logged in running the batch. In our case this is not a problem since we are using an ID that is just for our IT Desktop Support.
Hope this helps others that need to do functions like this. The batch could easily be modified to perform file functions, such as a Delete, Rename, or Copy for each profile on a system.