Veotag allows you to add this functionality to any of your video or audio from within their embeddable player. You can upload content (WMV, FLV, mp3) from your computer or via URL. Anyone can sign up for an account, upload content, publish, and start tagging points in the programming. The Veotag player wraps around the content, displaying time stamped comments along the right hand side that link to interesting segments, as chosen by the publisher. You can see an example of the player on a speech by Guy Kawasaki here.
Veotag has a search engine for the tags, which is also indexed by the major search engines. This index can then be transmitted to an ad serving engine for targeted advertising around the audio or video.
Readers interested in incorporating deep tagging into their own media should also check out Click.tv's video deep tagging widget with comments.