I code my site by hand... each and every page... for these same reasons. I need to figure out templating because it has become quite tedious to update links and I'm only at <50 pages!
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.
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...
