I've recently switched over to gnome-shell on both desktop on laptop. I hit a few usability hurdles, but have overcome most of them, so I thought I'd share some knowledge here (since I know many people have this same question). Gnome-shell uses Nautilus to manage the desktop. Nautilus only allows you to set a single wallpaper to use on both monitors, which is a bit unfortunate. To fix this, we first have to tell Nautilus not to manage the desktop. To do this install Gnome-Tweak-Tool:
After running gnome-tweak-tool, go to the "Desktop" tab in the left-side panel and then turn off the setting "Have file manager handle the desktop".
sudo apt-get install gnome-tweak-tool
Next install Nitrogen (our new wallpaper-setting application):
Nitrogen allows you to pick wallpapers from your hard-drive and set them to individual monitors, etc. To make sure that these wallpapers are restored after you reboot or logout, we need to tell Gnome to run nitrogen --restore at startup. To do this, run:
sudo apt-get install nitrogen
Here you can add a new startup program. In the command box, enter "nitrogen --restore". This will cause nitrogen to be run at startup and your most recent wallpapers to be shown on the desktop.
Hope this helps someone