With Sphinx-doc, you can create a bunch of ReStructureText files, with an index.rst file which includes a table of contents macro that auto generates a table of contents from the other included files, and a conf.py that acts as a compilation config. You can then compile the lot into a single python-doc-style site, complete with index, navigation tools, and a search function.
Is there any comparable tool for markdown (preferably pandoc-style markdown)?
Some static site generators that work with Markdown:
I think none of them use pandoc (maybe because it's written in Haskell), but they all use an enhanced Markdown syntax or can be configured to use pandoc.
Other interesting ways to generate a site from markdown:
Engines that use Pandoc:
The definitive listing of Static Site Generators
A good overview of static site generators: http://staticsitegenerators.net/