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I really like M2HTML, which automatically creates HTML documentation for MATLAB m-files and toolboxes. It quickly gives you a view into all of the files in a related project, including dependency/cross-reference information. This is useful not only for documenting your own code, but for getting greater insight into code written by others. I've seen a few different tools which perform this same basic task (including one I wrote several years ago which will never see the light of day again), but none with the polish or thoroughness of M2HTML.
The easiest way to get started is to follow along with the great online tutorial, located at http://www.artefact.tk/software/matlab/m2html/tutorial.php