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I recently abandoned my Pending folder and pretty much all other organization actually in email.

Instead, I write my task in OmniFocus as something like "Investigate bug re widgets glowing green instead of blue on alternate Thursdays. Reported by John Smith in email of 8/22/08." If you're clipping the whole email then you wouldn't even need to type any of that. I prefer to have the task described as a one-liner like this; for some reason, I don't much like having the whole email in OmniFocus and I prefer to go to email to get the original email if and when I need it.

Once the task is entered, I archive the email immediately into a formless "Mail 2008" archive. When I get around to the task, it's easy to search the archive for John Smith and 8/22/08. I don't bother to actually delete the email, because I think it's just not worth the trouble to decide whether I might need that email again, and since my archive exists purely for searching, it doesn't matter how much email is in there.

Gardener