Apple - Get Instapaper to save blog comments with article

Instapaper uses various filters to figure out what to strip from the page and which content to keep (Coding Horror configuration is here).

My only suggestion would to be to write a script which takes the content + comments, puts them into a new page wrapped in a div which has the class instapaper_body and saves that to Instapaper.

As mentioned in the previous answer, Instapaper deliberately doesn't copy comments. One solution would be to copy all the text, and email it to your Instapaper email address (which can be found by logging in, then looking here http://www.instapaper.com/extras - 3rd item down.