Madison Bicycle Federation told me that the bike registration isn't at all useful for finding stolen bikes. The only thing they really use it for is contacting people who have left their bikes on temporary racks outside of large city events.

I've heard of a lot of people keeping their data in the handlebars, but I don't know how valuable that would be if you aren't catching someone in the act. In my experience, the best defense is a group of friends keeping an eye out.