My employer limits the size of our email accounts, so I need to keep it clear. Whether or not you move it out of the inbox, you need a reliable way to mark whether you've processed each mail. My routine is:
1. Cut & paste all the inbox to a "process" folder on the hard drive.
2. Go through the mails in "process", dragging to my task list where I can't deal immediately
3. Cut & paste the "process" folder to my "reference 2009" folder. (This is the "processed" marker).
You can't get inbox to zero, if you are as popular as I am (?!), but you can keep it current and you can keep your "process" folder at zero.