Timelinely is a new free tool that easily lets you create an interactive experience for any YouTube video.
You just copy-and-paste the url of the video and then can easily pick moments in the video where you want to write added comments, annotated with an image, or add a link for more information. You can also interact with views through a comments section (you have to be registered with the site to leave comments).
They don’t yet have an embed feature yet, though say it’s coming soon.
You can see some things I did with a video of me talking about student motivation here.
I’m adding this info to A Potpourri Of The Best & Most Useful Video Sites.