The move from Gnome 2 to Gnome 3 breaks a previously working setup of org-protocol. Otherwise the instructions on the org-protocol page are still valid, but the Gnome integration part has changed. Previously, you were supposed to run these commands:
gconftool-2 -s /desktop/gnome/url-handlers/org-protocol/command '/usr/local/bin/emacsclient %s' --type String gconftool-2 -s /desktop/gnome/url-handlers/org-protocol/enabled --type Boolean true
The Gnome system has given up on the protocol handler thing altogether. To get similar results, you’re supposed to use Mime types. This page shows how it is done; the only difference to how it was done previously is, that you should add a file called “org-protocol.desktop” to “~/.local/share/applications/”. These contents work:
[Desktop Entry] Name=org-protocol Exec=emacsclient %u Type=Application Terminal=false Categories=System; MimeType=x-scheme-handler/org-protocol;
After creating this file, you should run update-desktop-database ~/.local/share/applications/.
This was the only change needed to restore the org-protocol-functionality on my system after an update from Debian Squeeze to Wheezy.