The question is a simple ETL task; take email as the input and output to a document. I have seen powershell able to access Outlook folders, and once you have it in powershell you can pretty much do what you want with it. You might be able to follow threads, only include missing blocks of text, ignore signatures, etc.
The real question is why make the effort of converting the emails to documents when, really, who is going to look through it? If someone is trying to find out where attribute FooBar is being set in program JarJar2001, how are they going to know which document to open? You need a good search engine, and the best ones are in knowledge management applications. Look at OpenText or Hyland or any other ECM app, or get Altiris to at least index what you have.
If the company isn't willing to take knowledge management seriously then neither should the OP.