If you want to make exact duplicates of floppy disks or drives, you'll want to pick up a copy of Apple's Disk Copy.  You'll want to get both version 4.2 and 6.3.  You'll find that a lot of Macintosh software is stored as a .img Disk Copy disk image file, it's the preferred archival format.

Furthermore, you can use Disk Copy to make a .img file that you can just copy to a FloppyEmu.

You'll also want to get a copy of Stuffit Expander version 4 or 5.  This can be a Catch 22 because you'll often need Stuffit to unstuff Stuffit.  Heh.  Stuffit Expander was the most popular compression tool on the Macintosh, and you'll run into a lot.