(Applies to iOS 6 and earlier).
Open In appears to have a limit to the list:
10 items in iOS 5
25 in iOS 6
Once it's full new applications will not show. The solution is to delete applications you don't use with "Open In" from the iPad or iPhone, and then others you can use will appear on the list. Once that is done you can reinstall applications you have deleted as the list seems to be in application installation order.