I thought of some locations that I don't know where they are:
Jake's House (is the one in Savannah and Tree Hill the same?)
The hotel where Carrie took Jamie (someone mentioned they stayed there but I don't know where it is now)
The hotel where Nathan went to see Deb in 310 (I think)
There was more, but I can't remember now.
Also when Peyton went to visit Jake in Savannah, was it all filmed in Wilmington? 'Cause they took Jenny to a park.