I have used a program called emailSTRIPPER from PaperCut software for years. It's great! It is only one EXE file, so it works great as a portable program. I thought I'd mention it so that maybe someone will package it for PortableApps.com. Here is some info about it:
Copied from http://www.papercut.biz/emailStripper.htm
emailStripper is a free program for cleaning the ">" and other formatting characters out of your emails. It will restore "forwarded" or "replied" emails back to their original state so they're easier to read.