Many apps write their data to the registry. Some also install their own libraries and whatnot to other folders. Apps like these will not typically relocate well by just a copy/paste from a backup: they need to be reinstalled. The only *easy* way I have ever seen to transfer these kinds of programs intact is to do a direct upgrade from Vista to 7.
Of course, some apps (Eclipse comes to mind) install everything right there in the program’s directory. Those types of programs will be the least-affected by a manual transfer to a new installation.
That’s been my experience! 🙂