Mail.app smart mailbox, how to negate a search filter clause (_not_ flagged)?
How can I negate the search criterion: "is flagged"?
I need all messages in a given mailbox, whose flag is not set (i.e. they are not flagged).
I would create a smart mailbox containing all Flagged items, and then (this is the one you want) a smart mailbox with the 'Not In Mailbox' option to return all the items that are not Flagged, and thus not in that mailbox.
Create this first: 
Then for the mailbox you want, create this one:
Worked for me in Mail 4.6, OSX 10.6.8.