There is now a Chrome Extension Reply To Many**Reply To Many** that allows you to Reply To Many emails at once while maintaining their individual threaded history. It works not by selecting individual emails but by applying a label to them, and it can use a variety of "responses" created as Drafts. (https://sites.google.com/site/replytomany/home/how-to-useHow to use).
This page is still for the now retired GMailGmail Gadget but it's still valid for the Chrome Extension. And yes, it was written by me.