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MacOS X people might want to investigate Eastgate Systems Tinderbox. Can handle the navigation links for huge ad-hoc Web sites using a local template then generate the Web pages.

I use Linux at home, and use a couple of bash scripts to make the index page and navigation links on individual pages that I write in markdown (but can hand edit html if the mood takes me).

Windows: powershell? A few scripts for indexing?

There are also large, flexible applications such as jekyl that can generate static Web sites.

Lots of static-site generators to choose from. Jekyll's the most popular choice. Link: http://jekyllrb.com

Since you mentioned Jeckyll, I also want to mention Octopress, which is based on Jeckyll http://octopress.org/

It's one of those things that every time I look at templating, I get overwhelmed and my procrastination says that the time it would take me to learn templating would be better served coding the site...

If you like Python, Flask is good. This article is useful:

https://nicolas.perriault.net/code/2012/dead-easy-yet-powerf...

I looked at Flask once. Not sure why I didn't return. This article is great. Thanks!.