OEM nav systems give you a stock look and finish, usually integrate well with the cars electronics, no wires or unsightly atennas. Drawbacks are, not transportable, no POI databases for speed cameras etc, can be expensive.
PDA nav systems can be used for other things, but integration into the vehicle is not as good, fiddly to use and need power for long journeys. Difficult to see in daylight. Sometimes dont carry all the maps you need, so have to swiicth maps on long journeys. Can have trailing wires etc. Benefits, portable, carry between vehicles, import POI databases for speed cameras, can be used for work. On the whole cheaper.
Thats about all I can think of.