Over the last year or so I've seen various announcements on the Clojure discussion list and other places about tools for documenting Clojure code. These range from full-on literate programming systems like Marginalia, and the tool being used to create the book "Clojure in Small Pieces" (or even emacs org-mode), to more conventional Javadoc-style solutions like Autodoc, and Javadoc itself which reportedly can be used with Clojure. A google search turns up various others, perhaps a few that deserve more attention, and for sure some that are just personal utilities for generating docs. My question is what are the best documentation tools, and what are their comparative strengths and weaknesses based on your experiences using them? I have not used any documentation tools to date, and am interested in experimenting with one or more.
I really like Marginalia if you want to take something like a literate programming approach. Marginalia traverses your source code, and produces an html formatted version with comments set beside code in a very clear text. Comments can be markdown formatted, making for a very readable final document. When reviewing source code that I've written some time ago, I find Marginalia really helps. Here's an example made from the Marginalia source itself.
Note that this differs from the original literate programming workflow, where you would write a file and source code is generated from that. With Marginalia, you write a regular source code file, and it's the documentation that's pulled out of that. The output is similar to what one might expect from literate programming, but this way you can still expect syntax highlighting in an editor, without any special literate programming support.
It interoperates with Leiningen, and I believe cake, though I haven't tried that myself.