Great example of combining the physical and the digital. Students took pictures of paper projects and then used Explain Everything to explain their dioramas.
Technology Integration Matrix with video examples for every topic and level of integration. Not iPad specific, but a great place to start when integrating technology.
This is a great article from UX Magazine. It does a great job defining interactivity and gives video examples of eBooks and eBook apps that have value.
Wondershare lets you edit PDFs from a Mac. It is less expensive than the full version of Acrobat. A great classroom example came from an EdTechTeacher summer workshop participant. She created a Wordle, which she saved as a PDF. Then she inserted a QR code into it that linked back to additional information on her blog.