Whoa, thanks! I hadn't seen any of those. Those all produce some really nice output.
Ultimately, I think the two can and should coexist. The benefit (and, I guess, potential drawback) of the OmniRef/RapGenius approach is that it allows the whole world to comment on code (and perhaps ask questions as well) versus generators like Docco/Rocco that (of course) can only display comments in the code that are provided by the code's maintainers.
Genius.com has a feature where they have verified contributors - for example, Genius/GZA from Wu-Tang sometimes explains his own lyrics on there. Those comments are displayed much like everybody elses' comments but are given special visual prominence because they're assumed to be authoritative.
OmniRef could do something like that too - longform inline comments could be displayed on the sidebar (ala http://coffeescript.org/documentation/docs/coffee-script.htm...) as a part of the stream of comments, and given special precedence.