The University of Minnesota has developed a wonderful tool for annotating videos called VideoANT. The program allows individuals to place markers in a web-based video and then add comments. This is a great way for instructors to direct student attention to key points in a video, or to ask students to find key points and comment on them. The link to the annotated video can then be emailed, which would allow students to submit their annotations as an assignment.
It's extremely easy to use. When you first go to the site, you can watch and experiment with a demo video. It's a great way to become familiar with the program, and takes only a few minutes to master.
One tip: I would put the marker (or have students put their markers) at the beginning of a point of interest, rather than at the end or middle. The markers can be moved at any time.