According to the Kitsap Pumas (linked above) they automatically qualify for the 2012 Lamar Hunt US Open Cup since they won their division. Joining them would be the Portland Timbers U-23 side, as they were the best remaining American team.
Other qualifiers based on last year's standings in the PDL (and assuming that this is true for all PDL divisions) would be the Michigan Bucks, Chicago Fire, Des Moinse Menace, Real Colorado Foxes, Long Island Rough Riders, Reading United, MPS Portland Phoenix, New Hampshire Phantoms, Carolina Dynamo, Northern Virginia Royals, Laredo Heat, Chivas El Paso Patriots, Mississippi Brilla, Central Florida Kraze (now Orlando City U-23), Fresno Fuego, Ventura County Fusion
Now that would be 18, so I may be jumping the gun. The only thing we know at this point is that the Open Cup will be changing.