YouTube has a built-in tool for adding annotations to videos that you own. Open the video editor in your YouTube account and you can add notes, including notes with hyperlinks to other videos, to your videos. Directions for that process are available here.
eduCanon is an excellent service for creating, assigning, and tracking your students' progress on flipped lessons. eduCanon allows you to build flipped lessons using YouTube and Vimeo videos, create questions about the videos, then assign lessons to their students. Once you have found a video through eduCanon you can add questions to it at any point along its timeline. Students need to answer your questions before they move on to the next portion of your chosen video. You can track your students' progress within eduCanon.
VideoNotes is a neat tool for taking notes while watching videos. VideoNotes allows you to load any YouTube video on the left side of your screen and on the right side of the screen VideoNotes gives you a notepad to type on. VideoNotes integrates with your Google Drive account. By integrating with Google Drive VideoNotes allows you to share your notes and collaborate on your notes just as you can do with a Google Document. You can use VideoNotes to have students submit questions to you and each other while watching videos. Of course, you can insert questions into the conversation for your students to answer too.
Blubbr is a neat quiz creation service that I have raved about since I tried it for the first time nearly three years ago. Through Blubbr you can create interactive quizzes that are based on YouTube clips. Your quizzes can be about anything of your choosing. The structure of the quizzes has a viewer watch a short clip then answer a multiple choice question about the clip. Viewers know right away if they chose the correct answer or not.