This could be the best $.99 spent on an app. Tools 4 Students includes 25 graphic organizers that can be annotated in the app and then shared via email.
Though $4.99, this app allows you to annotate video. For PE teachers, coaches, music teachers, science teachers or anyone else looking to make notes on physical actions
This free eBook is available for download and provides a great interactive resources. Each section ties into some aspect of Bloom's Taxonomy and provides additional information to support iPad integration into the curriculum.
This app, for $4.99, allows students to create their own animations. Though the app has an associated cost, the web version (http://doink.com) is free. Unfortunately, the web version won't run in Safari on the iPad. Cool regardless.
Adobe Reader has some great features - such as inserting a signature or filling in forms. However, when sharing out completed forms or PDFs with annotations, the notes do not appear. It seems as though this is best used if annotating and then printing.