Is there a way to use colors to differentiate nautilus windows that are viewing content on the local machine and nautilus windows that are viewing the content on remote machines?
It would help my organization if I could easily distinguish among different nautilus windows.
At the moment there is no way to make this sort of setting, you might want to suggest it as a feature request on Launchpad or brainstorm
The closest you can get, I'm afraid, is to edit your theme manually.
Look under
/usr/share/themes/theme_name/gtk-3.0/apps/nautilus.css
and
/usr/share/themes/Ambiance/gtk-3.0/gtk.css
You can change the colors manually using web colors
http://html-color-codes.com/
This is long way from what you are wanting.