I mostly use my own tool that I wrote. I use it to create REXX scripts to regenerate various individual folder trees; I've never tried it on the entire desktop at once, but it might work.
I never released it publicly before, as it's got significant limitations. It mostly depends on WPTools.DLL to query object properties, and WPTools so far hasn't been updated to recognize certain late additions to WPS setup string syntax. I was meaning to try and tackle that, but I never got around to it. Right now I don't even remember what features are missing, although next time I do a restore I'll probably rediscover them

.
The source is in the VXApps repository on NetLabs, and I just put a current (very much alpha, not properly tested)
build here. It's pretty simple: just drag and drop a WPS folder into the window and it'll generate an object tree of all its contents. You can then export the results to a REXX script or a couple of installer-specific formats which I've never really tested.
If you want it to save custom object icons then you need Rich Walsh's OO.EXE installed somewhere (eCS has included this program for years). I just added this feature to the latest version and it hasn't been tested extensively. If you don't have OO, then the program should still work but custom abstract object icons won't be saved.
Provided mainly for the curious and the daring. Absolutely no warranty!