You didn't say what version of Windows you're running. There's nothing wrong with the "Windows uninstaller". It unstalls everything it's told to uninstall. The problem is with idiots who write uninstall routines that don't properly remove all changes that have been made to the system by their installation routines. In Windows XP you can use the System Restore feature to get around that issue, but that approach does have limitations.
The point I'd like to make is that, if you don't choose your options carefully, the use of a third party auto-uninstaller to "clean up" Windows can quickly make you an expert at reinstallation of the OS and all of your apps.
Although there's more work to my method I use a little freebie utility called InCtrl5 (PC Magazine -- they should be useful for something, after all) to monitor the installation of new applications and drivers. It provides a list of changes made by the installation routine in system file complement and registry hives. I use that to reverse changes manually, if need be. Harder, but safer.
- prosaic