Some newer and higher-end cars even use proprietary crypto keyed off of the VIN number and a shared secret to protect from access by third-party tools. There's a good-sized cottage industry in breaking proprietary ECU protocols and crypto, because there's a solid niche market in selling mechanics one $20,000 "multiflash" tool to replace their ten $10000 manufacturer-provided "diagnostic systems," especially in the high-end exotic market.
I was able to find enough resource online to build an ISO OBD-II scanner as my seventh-grade final project, without needing to resort to hunting down the standard. Today there are even open-source projects like http://en.wikipedia.org/wiki/OBDuino which can provide a solid code-based understanding of the three old OBD signaling types (PWM, VPW, ISO), as well as the basic protocol.