I'm looking for something similar to what you would find at the front of a paper book. In other words, something that allows for arbitrary static ordering, not just by date or alphabetical ordering.
I've seen heading based plugins that generate a TOC for a post or page, but not a whole site.
I've also seen category based plugins that produce something similar to a index that you would find at the back of a book. Unfortunately the sort order cannot be controlled.
I had a look at the WordPress database structure and didn't see anything that looked like it would be used for building a table of contents.