A long, long time ago, Mark Kimes made this work in Library (an old add-on component to Moodle).
He made it so that pages had their own private comment glossaries.
In order to comment, the author opened a comment window, then grabbed a word or phrase from the text as a title.
(in this case, the author might choose Mark Kimes as a title and then comment upon how he is a brilliant programmer who loves motorcycles).
The word/phrase became highlighted on the page and a comment page opened at the bottom of the screen with the corresponding annotation #anchor-style.
Another cool thing was that pages were all versioned. In Mark's Library every page was a wiki page but with different writing permissions. In this way, course resource pages were commented upon/annotated by students and teachers; whereas student journals were commented upon/annotated only by teachers with read/write permissions. The comment author could choose to "stick" the comment to the page
forever (maybe a first draft grade comment), or to allow the comment to
stick tight to that particular version of the page.
It was pretty cool, but the code was very different from Moodle code.
I'm pretty skeptical that this could (or should?) be considered for Moodle; however, one thing makes it tantalizing: at one point, Eloy was looking to see how filters (like glossary filters) might apply to particular activities and courses, rather than just site-wide installations. Maybe that notion could be extended for this kind of annotation system (i.e. a comment/annotation glossary is attached to a student's blog by the teacher, or to a web-page resource for annotation by students)...
Pause -- Deep breath
I can't believe I've written such a greedy feature idea in these forums. Bad Tom. Bad, bad, Tom. This is while I'm still baffled and excited about the changes happening in 1.5. Have you guys downloaded the development stuff from CVS to play with? Have you seen the way the css stuff is just changing the way EVERYTHING looks and feels? 1.5 is not your father's conservative Moodle. Vroom. And the blogs in 1.6? -- really, really cool.