Good Fences Make Good Neighbors Act of 2006 - Amends the USA PATRIOT Act to authorize a border state (a state that shares a border with Canada or Mexico or a political subdivision of such a state) to use up to 75% of the minimum amount allocated to the state under the state and local domestic preparedness support grant program to build a physical barrier near the U.S. border to deter illegal crossings and for incidental costs.