If you use Apple Mail, you handle projects, and you're not using MailTags...what's wrong with you? :-)
Seriously, if you haven't heard of it, check it out:
http://indev.ca/MailTags.html
This little add-in to Mail adds a tagging panel to each message, where you can assign a Project, Keywords, Priority, Due Date, etc. It integrates with iCal, supports AppleScript and SpotLight, and is all-around wonderful (I have no connection with the company.)
I know the Omni wizards could think of awesome ways to integrate this with OF (and OmniPlan too!) Other third-party programs, for example iGTD and the MailSteward archiving program, already do.