MailTags is a great way to organize your Mail. It allows to tag each message with specific Keywords or assign it to one or several Projects as well as create reminders and notes associated with an email. The good news is that now you can show OmniFocus projects in as your MailTags projects. In this way you can make sure that your projects are named consistently in Mail and in OmniFocus. Tick a box in the Mail Preferences under MailTags:
Although 95% of messages do not require such organization (they are either not important or can be easily found through Search), I find that sometimes assigning emails to projects makes a lot of sense. Primarily it relates to intensive, long projects where a lot of participants exchange a lot of emails (I only have about 5 such projects running at any given time, for comparison I have some 40-50 active and 20-30 on-hold projects in OmniFocus). The fastest way to do it is naturally through using shortcuts created by MailActOn, another app from Indev. It helps that MailTags use OpenMeta Tags and thus messages can be found even from outside Mail!