It refers to the active 3% of Americans, at any given time, who fought against the British forces during the American War for Independence. It also refers to the estimated percentage of Americans that exist at any point in time who are willing to use force of arms to correct a tyrannical government and restore liberty to the American people as was envisioned by the Founding Fathers.
"The tree of liberty must be refreshed from time to time with the blood of patriots and tyrants. It is its natural manure." - Thomas Jefferson
"Threeper" and "Three Percenter", while applicable to Americans in the past, are relatively new terms to the general American populace. They particularly apply to the patriotic movement that has arisen in the face of the increasing power of the federal government that is present today. It is not a movement of extremists; rather, it is a determination of Americans loyal to the original intent of the U.S. Constitution that that document will be upheld by, and for, the American people.