I realize the question is stale, but for the benefit of Google: Matlab has a built-in feature for that. You write your comments in a certain style (a la JavaDoc) and they get picked up by the help and doc functions. It can be used to document classes, properties, and methods. It is surprisingly complete, yet a little finicky. The doc is here:
http://www.mathworks.com/help/matlab/creating-help.html