Hi,
Examples folder contains the module examples (if any). Helper contains the helpers (i.e., classes meant to ease the setup of other classes). The model folder is where all the classes of a specific module are. Finally the test folder contains unit testing classes, which are used by a special script, and whose aim is to test ns-3 consistency when we do code changes.
This is a short summary. However I'd strongly suggest to read the tutorial and the manual (both are available in the ns-3 website).
T.