Custom emblems can be created by putting the pngs in ~/.icons/gnome/48x48/emblems/emblem-<name>.png and creating a file called emblem-<name>.icon in that same dir which contains:

[Icon Data]
DisplayName=<name>

New emblems don't appear until a logout/in happens, although the Nautilus emblem dialog doesn't suffer from this problem. Must be a trigger somewhere.

Nautilus' side panel can be used to list all available emblems and then adding them to files is a matter of drag and drop.