Run iTunes installer and it will give you 2 options, 1 - Repair iTunes installation, 2 - Uninstall iTunes.
If you have not got a copy of this you will need it anyway to re-install iTunes.
Any way no matter what you will need to take ownership of the folder Apple before installation.
I did it before uninstalling iTunes as the first step.
The directory in Windows 7 is :- C:\Program Files\Common Files\Apple
More than likely the same in Vista and possibly the same in XP, but XP shouldn't have the ownership issue.
If you go to this webpage :- http://www.sevenforums.com/tutorials/1911-take-ownership-shortcut.html
it has the explanation in 2 steps and you can download the file to take ownership.
Once this has been done then the files and folders under Apple folder can be modified during the uninstall and/or installation.
We pay good money for software that has major flaws, you would think Apple and Windows would know how to resolve it, instead they are more concerned about looking after themselves than serving customers.