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There are many note-taking and annotation apps listed here. 

Notability is an iPad app for note taking that allows collaborative (or not) notetaking with sharing options. Plus it works with Dropbox (cloud storage)

Using your gmail account, you can watch YouTube videos and take notes at the same time (on screen) with VideoNot. I see lots of potential here.

PaperHelper is aniPad app that allows split screen--search web and take notes on other side ($1.99). This app really makes research online quite easy. Recommend.

Lots of note taking strategies are discussed on this website, many with handouts and examples.

Livescribe (reviewed positively in NY Times 8-19-10) allows the writer to take notes that are translated to computer; can also record and play back. Lots of potential, though a bit pricey (around $200--probably will come down, if we are patient!).

I searching through our old posts and found this one. The pens have come down in price, I bought one last fall ($100). My principal also bought a dozen or so with multiple paper packs (an educator bundle). I am using them in the fourth grade tier 2 intervention group for fluency. The students use them to record their reading, then they can listen to them selves to determine expression, monitor their time, and answer comprehension questions (again listening if they need to). I use them in 6th grade for literature circles. The students initial when they talk, so I can go back and tap their initials and evaluate their questioning/discussion. Some of my teachers use them for running records to share with other teachers and parents too.