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Here is the site for you when having studnets watch YT videos or other videos.  http://www.videonot.es You can watch video and take notes at the same time to the right of the video.  All notes are synchronized to the video and save to gdocs.

Free application that provides users the ability to document resources, bookmark sites, provide annotation, and has iOS app option too.  No Safari bar option available. 

Student created site for easing the process of taking notes in class.

SoundNote is the best way to take notes on your iPad. It tracks what you type and draw while recording audio, so you'll never worry about missing an important detail. While playing back your recording, just tap a word; SoundNote will jump right to that point in the audio. Use SoundNote's powerful drawing tool for quick sketches. It's easy to edit them, too. Tap a drawing to select it, or tap twice to select an individual stroke. From there, you can drag it to wherever you want, or tap "Delete" to get rid of it. Use two fingers to zoom and scroll.