Hey, nice links! I remember looking (briefly) for Perl-based literate programming tools a few years ago and not finding them. Thanks for these links.

My ideas for using LyX are quite similar to the basic notions behind literate programming. However, I do not wish to expound upon an algorithm. My interests are more focused on interleaving code into my research notebook. It's like, "Here's a thought" followed by the code to test that thought and produce a figure or two, which are embedded into the research notebook. Then, "Hmm, I expected X instead of Y..." followed by more code, and figures, etc. The exposition shows the flow of ideas from beginning to end, providing a context for the code. In this respect, it's close to iPython notebooks than literate programming.