At least initially, we will use the GNU Texinfo system. Texinfo, though perhaps not fantastic, is not too bad. Printed output is nice thanks to TeX, and tools exist for converting the Texinfo source code to PostScript, PDF, Info, HTML, and more.
We might find it useful to add specific Texinfo markers for Common Lisp, such as "@generic-function", "@method", etc. In that case, we either have to modify existing Texinfo translators to take those markers into account, our write our own Texinfo translators, which should not be to hard, aside from the fact that the Texinfo specification is not as formal as one might have wanted.
One advantage of writing our own translators is that we could use a structured in-core format for the final result, as opposed to (say) Info, which is limited to what can be put into a file. Our own format could use CLIM presentation features that would allow us to jump from documentation to code, for instance.
At some later stage, we might want to invent our own Lisp-y markup language for documentation to take advantage of our Lisp tools.
See also the page on the application browser.