I'd go down the folder list you posted except for the product version. You don't want the settings reset after an update is released.
I'm actually moving away from the registry for user settings because of the debug/footprint factor. I'm currently only storing a few basic settings (window size, position, version of a data file) in the registry and I've run into more problems if an update goes bad or a user loses a second monitor and that is where the application was opening too. A few of them are saavy enough to understand regedit, but for the rest they have to do a reinstall, which is quick, but I think they grumble a bit. With the file based version, all I'd have to do is have them open up an XML file in Notepad and make a quick tweak.
In addition, I'm looking to make my application runnable off a USB key, and having the settings tied into the file seems much friendlier to that process. I'm sure I can do some code to check/clean the registry, but I think most of us are already tired of the registry clutter that seems to eat up our machines nowadays.
I know there are some security tradeoffs to this, but none of the data I'm sorting is that critical to that cause and I'm not suffering any performance hits due to the size of the app.