Is there a way to have Nautilus automatically use my FUSE file systems to (for example) open ISOs as folders, or archives as folders, or what ever other 'locations' FUSE supports?
Nautilus can't possibly 'know' any installed fuse driver because the fuse system does not advertise its drivers mount options and whereabouts by itself. There isn't even a common database defined where the installed fuse drivers register themselves yet.
Note also that the gvfs system handles URIs like
However, there are lots of nautilus-action scripts around that may accomplish what you need. And if you can type in the mount options by hand, a xfce-tool named