iTunes U - Post your most important materials in iTunesU for your students to access. Everything from reading materials, notes, videos, and notifications can be posted. Courses are organized and materials can be shared among teachers all over the world.
Evernote - This app is a wonderful organization tool for students and teachers that have "flipped" classrooms. Materials can be organized into folders, notes can be shared, and assignments can be turned in via Evernote. Evernote, like many other apps, can be accessed from multiple platforms (Apple, Windows, Android, Blackberry, etc).
Penultimate - A handwriting app that looks like paper and feels like writing with a pen/pencil. Penultimate syncs with Evernote and allows for students to take notes in multiple "notebooks" and easily share with others.
Skitch - Add images to Skitch then use the tools to annotate, add shapes, and save to Evernote. Edit images and communicate ideas fast with Skitch!
Edmodo - An educational application that is set up like a social networking site. Students can have classroom discussions, work on group projects, and share ideas.
Notability - This is a note-taking application for the iPad that allows students to organize their subjects into folders. Notability syncs with iTunesU and Dropbox. Images can be inserted and students can type notes of different sizes, fonts, and colors.
Ask 3 - Create a video including voice, images, and drawings and send them directly to your students iPads. Students can comment on the videos or ask questions leading to a class discussion. Students can also make their own videos to be sent out and receive their own comments and feedback.
QR Reader - Scans QR codes and takes the user directly to the website needed. Students can access learning materials via QR code.