The OBD thing basically has to do with keeping the air you and I breathe clean. There are a lot more differences between the different OBD's than many people think. I will elaborate more on OBDI and OBDII. The difference between the two is that ObdII is more advance in what the ECU can do. The ecu has incorporated testing parameters to test every emissions system on the car before the car is started and while it's cruising down the highway and the driver doesn't even notice it happening. When it finds that something is not working right it throws a check engine light (MIL). OBDI never had this and if there was something wrong with any emissions system the driver never know something was wrong with the car. All the little things add up to a big problem as time goes by.
Now concerning motor swaps, the law states that the donor engine must be the same year or newer. The reason being is that manufacturers are constantly changing head design, cam profiles, intake and exhaust port flow charateristics, etc... to increase efficiency and to reduce emissions. So newer engines are considered to be better in reducing emissions. Although a B16 head from 1990 may look identical to one from 2000, the newer head is by far better.