I have seen some examples where adaptive control is used to counter sudden changes in a system with great success. Since I find the subject quite interesting, I would like to learn how to actually implement an adaptive control loop, with the end goal being to write a flight controller for a quadcopter (this is something for the future though). I have found some quite good theoretical text-books on the matter, but not really any good in-depth examples or implementations. The methods that seems most interesting to me are the direct and indirect MRAC.
So in short: Where can I find a good in-depth example/implementation of an adaptive control loop?
First, I would recommend you to search and read some academic papers on what you are interested in. I believe there are many papers on designing adaptive control for quadrotors with implementations.
Second, in my opinion, it is not quite proper to apply adaptive control to flight control. Reason 1: Adaptive control usually are applicable to systems with unknown but constant parameters. In flight control, usually it is required to build a very good flight model before you start to design controllers. A flight model with unknown parameters is not acceptable. If there is an unknown parameter, in stead of designing an adaptive controller to handle this parameter, we should do experiments to identify it. Reason 2: flight control requires controllers to response fast. But adaptive control usually are applied to relatively slow plants such as industrial processes. It is possible a quadrotor crashes before the adaptive control can stabilize it.
So if the model is not highly nonlinear, PID, LQR, $H_2$, $H_{\infty}$ probably are good choices. If the model is highly nonlinear, you need to employ some nonlinear control methods such as feedback linearization, backstepping, sliding mode control.