Well... this isn't *totally* related to your post... but...
Supposedly we are working towards the goal where once again all apps will be fully self contained. Now we have the DLL and registry pain... if you try to directly copy an application you KNOW it just won't work.
But! Windows .NET is building a platform that will enable coders to compile in such a way that all necessary info will be held in the app folder. I've built a few apps like this and it's GREAT. You want to delete the app? Just delete the folder, no messy uninstall to worry about. You want to give the app to a friend? Just zip up the folder and send it to him, and they're up and running. The app needs to cache files, create files, etc? All self contained in the folder, so no worry about leaving a mess in other folders.
Of course there are concerns about copy protection. (I still say easy to do... when app is installed and asks for the registration key, just have that create an encrypted key-file in the folder tied to that computers UUID. The app will work when copied... it'll just ask for the registration key again).
Anyhow, the technology already exists. We'll see if anyone picks it up.
It just doesn't fix your problem today.