YouTube recently announced the addition of a video annotation tool. YouTube describes that users can add three types of annotations to their own videos: speech bubbles, notes, and spotlights. Links, which presently only point to other parts of YouTube, can also be added to annotations.

Update 1/30/2009: YouTube adds improved annotation interface.
Update 2/20/2009: YouTube adds global control for showing annotations in user preferences.
Update 2/20/2009: YouTube adds collaborative annotations.

More information can be found on YouTube Video Annotations.