Videonot.es will present you with a split screen. One that displays a video you assign and the other a text doc for note taking. When you pause the video it will put the time into the document so you know the exact place to return to for the note. Notes are saved to Google Docs and can be shared through your drive. Works with Khan Academy, Vimeo, and You Tube among others. Super simple and helpful.
Video Not.es Overview Tutorial
Give Videonot.es a try with one of these 3 mInutes Ted Talks:
How to Tie Your Shoes http://www.youtube.com/watch?v=zAFcV7zuUDA
A Story of Mixed Emoticons https://www.youtube.com/watch?v=eYyN_6GmzWI
Try Something New for 30 Days https://www.youtube.com/watch?v=JnfBXjWm7hc
8 Secrets of success https://www.youtube.com/watch?v=Y6bbMQXQ180
How to Start a Movement https://www.youtube.com/watch?v=RXMnDG3QzxE
Ideas for Using Videonot.es for Analysis, Peer Review, and Grading
Not featured here, but an additional helpful tool for flipped video lessons is EduCanon. With a teacher account, students can be added to your class with a code. For each assigned video you can create assessment questions inserted at various points within the video. Students must watch the video and answer the questions. They cannot fast forward through the video. You get a spreadsheet of data for each video logging not only correct respones but how long a student stayed on the video and how many times they replayed it.