I just got the most recent issue of IEEE Robotics and Automation magazine, which has a theme of quadcopters as robotics research platforms. There is a large article describing the various attitude estimation and control algorithms used in Arducopter, OpenPilot, Paparazzi, Pikhawk, Mirokopter, KK muticopter, Multiwii, and Aeroquad. If you want to know what the difference between what we are doing vs one of the others, this looks like a great resource.
There is also a great article by Robert Mahoney (of DCM fame), Vijay Kumar (from U Penn), and Peter Corke (Queensland U) titled "Modeling, Estimation and Control of Quadrotor". If you want to review first principles and the math basis for quad rotor control, this will interest you.
Several other interesting articles including one on the interface between autonomous and human control, and another on optical 6Dof Pose estimation.
It's free and the open source flight controller comparison article starts on page 34. Sample below: