but dislike my root window being covered in pointless file manager icons

I think you want the gconf setting /apps/nautilus/preferences/show_desktop: If set to true, then Nautilus will draw the icons on the desktop.

I was just about to post

gconftool-2 --type bool --set /apps/nautilus/preferences/show_desktop false

too

Aha, yes, that seems to have done what I wanted. Thanks!

(Bah. I actually looked in /apps/nautilus/desktop, but didn't think to look for a desktop-related option outside that subfolder.)