I was thinking in terms of this:
http://calibre-ebook.com/user_manual/cli/calibredb.html
calibredb lets you extract solely the comments and redirect the output at will; if you have some skill with Powershell you could write a script to do it all at the command line.
Or this:
http://sourceforge.net/projects/calibredbxtract/
Or saving the full catalog as a csv file and feeding it to Excel, Access, or your db app of choice to extract just the comments.
Ideally one would want the bookshelf to be able to display the full range of the book's metadata but that's not yet an option.