In my "Documents" folder, I just use the two folders created by TI-Connect and TI-Nspire Computer Link, "MyTIData" and "TI-Nspire", respectively.
Inside those folders, I think I have a "Development" one in the Nsipre folder which contains folders for each of my individual projects, and a folder "GCC4TI" in the mytidata one for 89 projects.