A multi-TeX-file thesis template with some introduction to simpler elements.

University of Oregon's Thesis and Dissertation LaTeX site.

It might be a bit under-automated, or a bit over-divided, as I'm not sure the abstract and the dedication need separate files.

A marvelously detailed, well-commented thesis package (even if it is in one document): "Using LaTeX for thesis writing..."

Using LaTeX for thesis writing at the University of Washington.

The author mentions he set it up as a single file in order to make file-sharing simpler, but it doesn't seem entirely clear how to set it up in the multiple-TeX-file format he suggests.