How to set nautilus to --no-desktop via gconf

Yes, in Gnome 3, Gconf is being replaced by DConf, which is accessed through GSettings. You can use dconf-editor from the dconf-tools package to explore. It's very similar to gconf-editor.

The entries your looking for are located at org -> gnome -> desktop -> background

Uncheck draw-background AND show-desktop-icons

No more openbox menu and wallpaper problems :)

The setting mentioned in Jo-Erlend Schinstad's answer has been deprecated and I can't find a new equivalent setting. A workaround is to let the file manager set the background but set the alpha to zero. The command for this is

dconf write /org/gnome/desktop/background/picture-opacity 0

or you can use the dconf-editor gui to set it as discussed in Jo-Erlend Schinstad's answer.

The setting to hide the desktop icons is still the same:

dconf write /org/gnome/desktop/background/show-desktop-icons false