What is the difference between the NetCDF and SAFE files?

The SAFE are the data originally disseminated by the European Space Agency. The SAFE format is basically a ZIP file with a collection of XML and other files. Within the SAFE file, the spectral bands are presented in the native spatial resolution of the satellite sensor. On the other hand, in the NetCDF files all bands are interpolated to the spatial resolution of the band with the highest resolution. This provides and image stack that is easy to use in processing.

Where can I find information on the SAFE format?

SAFE is a format developed by the European Space Agency for "archiving and conveying Earth observation data within the European Space Agency (ESA) archiving facilities and, potentially, within the archiving facilities of cooperating agencies.". Further information on the SAFE format is available at http://earth.esa.int/SAFE/.