In the BROWSER ID tab of the options, you should be 
able to type in your own HTML code to add as a footer 
to each captured HTML page. While I've never tried 
using anything but <!-- comments -->, I don't see why 
it would stop you from using true HTML code as 
well...assuming that the source webpages don't have 
any </body> or </html> tags in them.

- Corey