Do the shock waves from a supersonic plane affect general aviation planes?
Great question!  I am far from an expert in supersonic flight, but according to this NASA chat transcript, Ed Haering (an aerospace engineer at NASA's Dryden Flight Research Center in Edwards, Ca. who I would consider to be an expert) answers just this question and says that it isn't a problem for other airplanes:


  chetman1020: Do sonic booms ever disrupt other things in the air?
  
  Ed: Sonic booms can temporarily dissipate or accentuate a "Sun-Dog," the small bit of a rainbow off to either side of the Sun
  caused by high altitude ice crystals. Aircraft are not affected by
  booms from other aircraft.