When I used to work in application packaging (ahhh, the good old days), one of the common issues we'd hear about from our users was that "my PDFs no longer open in Adobe Reader" or "my image files no longer open in Windows Photo Viewer". The problem here is that two or more apps have a file extension associated with them. The first app is installed, and everyone is happy. But along comes app number two and it takes the file association, and the PDF/image file/document/whatever now opens in app number two by default.
This is a quick thing to show one user how to fix, but when it happens to thousands of users it can be a real headache, so it's best to know about these file extension clashes before you deploy your apps.
Here's how you can use ChangeBASE to check for file extension conflicts: