Vlfeat [1], the winner of the ACM MM 2010 open source competition, has excellent API documentations which are automatically generated from the source code using doxygen. As long as Caffe is participating the ACM MM 2014 open source competition (#127), it is worth creating similar high quality documentations for the public API.

[1] A. Vedaldi, B. Fulkerson: Vlfeat: an open and portable library of computer vision algorithms.