JKN features:Nothing to download, nothing to install
Compatible with all web-pages
in vivo – your comments are inserted between words, so nothing of the original page is obscured and your comments can be read in context.)
Multi-page support
permanent – even if the web page changes, your comments will be shown with the web page as it looked when you created the Annotation.
international – supports all character sets
optional button for FireFox allows you to even annotate password-protected pages.

From what I read in your blog posting, JKN would seem to be a good fit for the research community.

This ia an example of a research article with comments:

http://jkn.com/View?j=765171.167353029906&t=42