Passport is a verification program for 5.25-inch Apple II floppy disks. It can verify all unprotected disks and many copy-protected disks. It can also create a copy of the original disks in a standard 16-sector format, and optionally apply patches to the copy to help make the copy work properly.
Jeremy Barr-Hyde is already using Passport. Check out his excellent blog post documenting his archival workflow for backing up protected diskettes.