I use flags sparingly. I flag items that require a response, and I unflag them when I send the needed response. Flagged items remain in my @INBOX indefinitely, so I make a point of unflagging handled items, to keep my @INBOX clean.
SaneBox also gives me the option of forwarding a message to a special email address from which it will return to me later (as determined by the email address). The program also allows me to create special folders for deferring a message until a specified time or day.
My system identifies five categories of messages:
Quick response: The quick response category comprises email messages that require a one-off response and no further action (other than action that may arise in connection with a possible reply to my response). I deal with messages in this category immediately, responding in one or two sentences. The original message can then disappear from my @INBOX. If the author of the original message sends a follow-up response that requires action, I deal with the second message as a new item.
Thoughtful response: If a message requires something more elaborate than a two-sentence reply, I deal with it when time allows. If I have the time and the reference materials on hand for an appropriate response, I compose it immediately. If not, I assign it a red flag so that it remains in the @INBOX until I respond and unflag it.
Action required: Email messages that require action other than an email response don't belong in my @INBOX. When a message of this type arrives, I use OmniFocus to create an OmniFocus task, with a link back to the original message. This allows me to handle it within a single task-management system that keeps all of my tasks in one place. When I complete the task, I click the link in the note and open the original email message, which is ready to accept my reply if I choose to send one.
Informative: Some messages I receive are simply informative. If a message contains material that I may need to consult or cite later, I move the relevant information into my reference system. I use nvALT for this purpose, but you can use whatever your primary "bucket" is (Evernote, Simplenote, or the like). Each note receives a concise, accurate title and has three other components: the body of the information, a link back to the original email, and tags (or a notebook designation) associating it with the right project.
Everything else: If an email message doesn't fall into one of the first four categories, I delete it. If I suspect that I may want to find it again later, I mark it as read and let it fall out of @INBOX. I delete relentlessly, though, and rarely (if ever) have I regretted doing so.
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