LaTeX thesis post

Using Joel as a guinea pig, this seems to work relatively well. My thesis zipfile includes the main file, thesis.tex, which serves to define the basic document parameters, call the frontmatter file, then input each chapter (chapterX.tex), then call the bibliography file.

With these files, you first need to produce an ".aux" file by compiling thesis.tex in latex mode. If you are doing this on the command line, you'd just type
> latex thesis.tex

Then, you compile the bibliography file, thesis.bib, to produce "thesis.bbl":

> bibtex thesis

Then, compile the main thesis file twice to get all the cross-references right:

> latex thesis.tex
> latex thesis.tex

If you are not familiar with large latex files, during each compiling status there will be many errors/problems/subidealities. Usually this is signified by having the error reported and then a ?, and you hit return to tell the compiler to acknowledge the error and move on. (If you try to do this with my files you'll have to hit return several hundred times because of random "errors" and because all the image files are missing; if you want an easier time you can delete all but one paragraph of each chapter.)
I think that's the core of the stuff, I think I have formatted the files so that minimal changes are required. Frontmatter.tex sets up the formatting for the front page, you just need to change the date and names, and then calls abstract.tex, which you can change separately. Same for acknowledgements.tex, and obviously the number of chapters and appendices will vary. Joel has recommended Jabref and says it makes the references/biliography file pretty straightforward, but I didn't use that so you'll have to get instructions from him.