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.

The Best Introductory Overview to LaTeX (so far) "LaTeX Your Document"

LaTeX Your Document by Reed College's CIS Help Desk

While I don't have access to their Thesis documents, this has been the best overview and step-by-step introduction yet.  It does not address using LaTeX on different operating systems (Mac at home and Windows in the lab, for example).