I have built a number of Eddy Current brake dynos. I use an "old fashioned" analog control amplifier and Thyristor phase angle control system. I have not tried to use any type of pwm and digital PID control yet, but am interested in developments in this field for the future.
You may, however, be interested in this 8 channel Arduino data logger which I have built and have implemented on an Eddy Current Loading Dyno. My inputs are all converted to analog before being sampled by the Arduino. One channel could be reconfigured for a pulse input from an Encoder to log Roller Speed/ Rpm.http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1292480606/0
My personal feeling is that is would probably be a good idea to use 2 Arduinos, one for data logging of Speed/Rpm, Torque, Power, Temperatures, etc. and another to deal with the Control loop. This would make development of a new system much easier to begin with. You could use the analog voltage Roller Rpm output from the Data Logger as a Speed/Rpm input to the Control Arduino.