I recently discovered one approach to registering new protocols that at least work with firefox. By registering the "pseudo" MIME type x-scheme-handler/<protocol> with the mime system and the .desktop system, at least the firefox browser will suggest to start the registered program.
I just uploaded a version of vlc-plugin-bittorrent using this trick to support magnet: style links. I suspect it can be used to support bitcoin: style links too. -- Happy hacking Petter Reinholdtsen