Provide automatic filing capabilities see http://www.clearcontext.com/
Streamline the Inbox to focus on important emails
Turn your emails into actions and to-dos
Clear your Inbox quickly with one click filing
Organize work by Project so you know what's next
Johann Richard commented
Another a bit different approach is SimplyFile http://www.techhit.com/SimplyFile/ that does really smart filing based on statistical/Bayesian analysis of mails in folders and also allowing to file when replying to a mail or sending a new mail.