I believe that with iOS 6 - your list of apps to use with the "Open In..." function has been increased dramatically. It used to be you could only see 10 apps (and you had to do the delete/reinstall trick to show some, as Kevin mentioned).
However, with iOS 6, I've had up to 18 apps show in the "Open In..." window. You even get a paging function if there are more apps than fit in the window.
So, if you are seeing an app, make sure that it is capable of running the file you are trying to open. If it can't work the file, it won't show in the window.
Or, sometimes developers don't put the "Open In..." capability in their apps. If you know that certain app will run a certain file, but it doesn't show in "Open In..." - my best recommendation is to get back with the developer.
Marilyn