I've been poking around a bit and asking a lot of people a lot of dumb questions, along with reading a bit about the Arduino micro controllers.
There appears to be two options that I've found for a "shield" (a piece of hardware/circuit board that plugs in to the Arduino to expand what it can do) that connects up to the OBDII port and gives useful information to the Arduino, so from the looks of it decoding the OBDII port is a hard ware issue not a soft ware issue, it's also a problem that sounds like it has already been thought about.
Sigalabs | Vehicle OBD2 Shield with STN1110 IC
Is the shield that looks like it's going to be more useful as it sounds like it self recognizes the vehicle it's plugged in to.
2nd issue that I was not sure about but checked today was the TPS (throttle position sensor) and if the OBDII port would get a reading from it if the engine was not running, my reason for wanting to know this is if you are driving a plug in hybrid and only making a short trip you don't need the gas engine to be running but you still want to use the accelerator pedal and TPS to control the electric motor and thus drive the vehicle, as it turns out the TPS gives the computer and thus the OBDII plug a reading even when the gasoline engine is not running.