Here is a general description of the protocols and where they are used:
Motorola Binary (All ONCORE receivers) This is the native Motorola communications protocol, operating at 9600 baud, 8/N/1. Use of this protocol offers the richest command set and control over most of the receiver operating parameters. Most commonly used for timing applications
NMEA (National Marine Electronics Association) protocol is an ASCII text based standard operating at 4800 baud, 8/N/1. NMEA is a standard in marine navigation applications, and is used almost exclusively in Automatic Vehicle Location (AVL) and in vehicle tracking applications. It is also quite popular with hobbyists and newcomers to GPS since the data is output as human readable text that can be viewed with generic terminal programs (Procomm,etc.) receivers running in NMEA mode can also supply data to applications such as Microsoft Expedia Streets.