[sriggs]

Here's how I handle email. I use Apple Mail. I don't file anything. I leave everything in my inbox. I use a smart mailbox called 'Email to process' and it shows me only unread and flagged email. When a new message comes in, I do one of the following...

Trash it (and I'm finished)
Respond to it (and I'm finished)
Flag it (if I need to keep it in 'Email to process' while I decide what to do with it)
Send it to my OmniFocus inbox (to do later)

Once the email is unread and unflagged, it disappears from the 'Email to process' box automatically.

Later on, I process my OmniFocus inbox and file it appropriately. The send to OmniFocus inbox feature adds a link back to the original email so I can get right to the message when it is time to work that particular task.

When I need to refer to old messages, I use smart mailboxes to find and group the messages for me. For me, it's much easier than filing.