It sounds as though things have got in a bit of a muddle. Usually removing iTunes and related programs and doing and installer file clean up fixes this:
Download a fresh copy of iTunes and the stand alone version of Quicktime (the one without iTunes)
http://www.apple.com/quicktime/download/win.html
http://www.apple.com/itunes/download/
Download and install Microsoft Installer cleanup utility, there are instructions on the page as well as the download. Note that what you download is the installer not the program – you have to run it to install the program –All Programs>>Windows Install Cleanup
http://support.microsoft.com/kb/290301/
Now use the following method to remove iTunes and its components:
XP
http://support.apple.com/kb/HT1925
Vista
http://support.apple.com/kb/HT1923
If you hit a problem with one of the uninstalls don't worry, carry on with the deleting of files and folders as directed in the method.
When you get to deleting Quicktime files in the system32 folder as advised in the method, you can delete and file or folder called Quicktime.
Restart your PC.
Run the Microsoft Installer Cleanup Utility. (Start > All Programs > Windows Install Clean Up)
Alright, polydorus found the solution to our problem... follow his/her instructions below. I downloaded the Microsoft Installation Clean Up Utility, ran the program, found iTunes on the list and deleted it. Bam! No more problem. Great job, polydorus.
Remove any references you find to the programs you removed - strictly speaking you only need to worry about those programs where the uninstall failed.
restart your PC
Install the stand alone Quicktime and check that it works.
If it does, install iTunes.