Wired has an article

entitled "New Tech Protects Ancient Torahs" about two methods to create a "Safer" Torah:

First, the Universal Torah Registry:

the system works like this: A synagogue mails in a form with their contact information and the number of Torahs they want to place in the system, and the registry sends back a computer-coded template for each scroll. The 3.5- by 8-inch template resembles an IBM punch card, with eight holes arranged so their position relative to one another describes a unique identification number in a proprietary code.

A rabbi uses the template to perforate the coded pattern into the margins of the scroll with a tiny needle. To keep an enterprising thief from swapping the perforated segment with a section from another stolen scroll in some kind of twisted Torah chop shop, the registry recommends applying the code to 10 different segments of the scroll. Pollack says the code contains self-authentication features that keep a thief from invalidating it by just adding an extra hole in an arbitrary location.

Now if a crook tries to sell the Torah, the pattern can be mapped back to the ID number, which is linked to the rightful owner in a database. "It makes it harder to fence," says Pollock. "If your car has a VIN number, it's harder to sell illegally."

and an alternative system:

Machon Ot's system, the International Torah Registry, takes advantage of the handcrafted nature of the Torahs. Though the content is always the same, the position of the lettering varies from scroll to scroll, making each Torah as individual as a halachic snowflake. By measuring the distances between letters at certain standardized points, and entering them into a computer program, Machon Ot generates a 20-digit number that uniquely identifies each Torah.