A Mustang Dyno puts a load on the car and measures torque and figures the hp based on the torque measurement. A Dynojet measures by how fast you spin up the weighted drums. There are many other differences than just that, but that's the simple version. A MD will read about 10% lower than a Dynojet.
Some people say the MD is more realistic but if you're just looking to compare numbers of your combo the Dynojet is more of the industry standard for comparision. MD is also supposed to be better for tuning.