Then, if you must use it, reinstall it and be very careful during the setup - there are options for what files you want to associate iTunes with. Check only those that apply, and leave the rest blank.
Most likely what has happened is that you have selected a file that didn't have a program associated with it and when you selected itunes to open it you didn't remove the check beside the box that says use this program to open all files. You just have to go back and reassociate the correct program to the files.