The Appeals Courts Theory

Most of the cities with a Federal Court of Appeals within the city were hit. Washington D.C., which contains the US Supreme Court, was also hit.
1st Circuit (Boston)
2nd Circuit (New York)
3rd Circuit (Philadelphia)
4th Circuit (Richmond)
5th Circuit (New Orleans)
6th Circuit (Cincinnati)
7th Circuit (Chicago)
8th Circuit (St. Louis)
9th Circuit (San Francisco)
10th Circuit (Denver)
11th Circuit (Atlanta)

FBI Offices

Twenty of the Black Jack Map targets have FBI field offices. Hartford does not (it is 30 miles north of New Haven, which does), and southwest Utah does not. If Lawrence (not Kansas City) was targeted then the FBI office count is nineteen.

Population Centers

Eighteen of the Black Jack Map targets are the top 22 Metro Areas listed in the 2005 US Census. (New York NY, Riverside CA, St Louis MO and Tampa FL, if they had been targets, would have made a straight run of 22.) The population rank for other four metro targets are Kansas City/Lawrence (#27), Charlotte (#36), Hartford (#44) and southwest Utah (no rank). (The Columbus OH "target" is ranked at #32.)

Port Cities

San Diego, Seattle, Los Angeles, San Francisco, Philadelphia and New Orleans are all major port cities, and thus would serve as a point of entry for any aid sent by other nations. Based on this, the possibility that other port cities not already mentioned (Miami, FL, Portland, OR, Boston, MA, etc.) were hit or at least damaged in the attacks. The Chicago River and the I & M Canal connect the Great Lakes with the Mississippi River making Chicago a port city of sorts.

Military Importance

A major naval base is located in San Diego, and the city was once the headquarters of the Pacific Fleet (though this was before World War II). Denver is located close to the headquarters of NORAD, though other military installations are located nearby. Philadelphia is also the home of a naval base. Washington, DC, of course, is the home of the Pentagon. <s>There is a naval base north of Chicago (The naval base is Naval Service Training Command, Great Lakes and it is 35 miles straight North Northwest of downtown Chicago) , and the air force used to have a base at O'Hare.</s> These are no longer strategic. It is a major population center and still has large productive capabilities (manufacturing, steel, etc.).

Governmental Importance

Washington, DC is the capital of the nation, and, considering the attacks took place during a major Presidential address before both Houses of Congress, it is best to assume that most, if not all, of the government of the United States was wiped out. DC is also gone, implying that stronger or multiple bombs were used to make it "gone."

Atlanta and Denver are the only state capitals known to have been hit. St. Paul, MN, across the river from Minneapolis, while not destroyed, would have suffered damage and severe fallout. Whether or not the governments of those states were in the capitals at the time remains unknown. Langley Virginia, which is near Washington D.C. and Minneapolis are both major FBI headquarters.

Population: All of the cities listed are in the 500K - 1 Million + range.