Many people here have mentioned the microchip, but the problem I see is that you need special equipment to read it. Yes, you do need "special equipment" to read a QR code - a cell phone with a camera and internet access. But there are WAAAAY more people with cell phones than microchip readers. The other problem with a microchip is you can't see it. If you can't see it, how do you know it's there?
My husband and I were discussing the problem of what to do if the quilter does not have his/her own website. He thinks the solution is to have people register their quilts for a dollar or two (to offset the cost of running the website) and they could register their quilt. If the quilt is lost or stolen, the website activates the page linked to the quilt. Anyone who clicks on the QR code is taken to that page, informing them the quilt is missing, and is given information on how to return it. (I've actually contacted Maria from lostquilt.com about this.)
As far as actually PREVENTING theft, I honestly don't think there is a way to do that. Anyone willing to steal will find a way.