It occurs to me that we all build custom guitars here, and I've not heard of anybody coming up with a good unique serial number system. I've been dealing with an insurance company lately who's giving me suggestions on how to identify my fiddles and such, and of course the first thing they say is "Record Serial Numbers!" Perhaps if somebody provided that service, they could sell those numbers and assign them to owners. Maintain a database so there's no duplication, that sort of thing. Base it on a Julian date number with a short 3 digit derived extension to simplify it. You'd be able to refer to your 7th Les Paul as the ".294" build, or something like that.
Food for thought.