James Tauber notes some similarities between annotations, comments and trackbacks. This is the same similarity I noticed a while ago and was the impetus for the creation of the CommentAPI.
The same functionality as the CommentAPI is also available under Atom since comments are treated the same as entries. The equivalent of the CommentAPI under the AtomAPI is a PostURI on the entry. That PostURI on the entry can be found either by a link tag in the feed or via a link tag in the HTML header of the entry. Now matter how you find it, posting an entry to such a PostURI will create a comment/annotation/trackback for that entry.