Would it be possible to have a video (MP4, FLV, F4V, or some other popular format) contain a table of contents that the user can click to seek to different sections of the movie?
Option 1: cue points.
Adobe video formats do support cue points. see: http://www.communitymx.com/content/article.cfm?cid=124DB
Cue points may be added by the encoder or programmatic. The first option have a great advantage in accuracy, and the second one is more flexible.
Cue point will trigger an event so you can use it to link another video as well. see: http://theflashblog.com/?p=78.
you can find the cue points in advanced (say, when the app is loaded). See: This link (look for "Find cue points")
Option 2: live steam meta data
if you are working with live streams, cue points may not be what you need. However, there is a solution. Streams may contain meta-data in it. the meta data content is up to you and you may pass along xml or any other format with the relevant data on the next point position or the next movie position.
See: http://www.adobe.com/devnet/flashmediaserver/articles/metadata_video_streaming.html
Enjoy!