Here is what i have figured out :
The cheap solution like the scantool one, which has a small microprocessor in it handles all the ISO/OBD-II communication, comms with the pc is regular 9600 baud serial. This means that this solution is easier to make your own gui for. The Cables without any logic/"cpu" is dependant on your skills at programming a serial port for all sorts of weird stuff like 5 baud and 10400 baud.....not really standard rs232 speeds. However you can make it work with almost any ISO standard of OBD-II, since there is like 4 or 5 different ISO protocols used today.
Extended OBD-II codes are usually hard to come by, since they are manufacturer proprietary. So searching the net or maybe some local dealers will have some info.
You CAN control fuelmaps and other quite interesting stuff through OBD-II, but not in all vehicles. My car is a Citroen Xsara VTS with a Magneti Marelli 1AP ECU, and all vendors of tuning equipment say that it has programmable maps via diagnose plug (meaning OBD-II) One thing though, keep in mind that OBD-II as per the standard has no means of changing any values except clearing DTC's so it must be a proprietary thing again....as with many things in the automotive industry, but you will soon find that out.
Hope this can clear up some things :-)