I wrote my PhD thesis using the WYSIWYM (what you see is what you mean) editor LyX. This is a really nice front end for LaTeX (including pdflatex, xelatex, lualatex etc). I used the utthesis.sty file as the starting template, but modified it quite a bit to meet the Queensland University of Technology (QUT) guidelines.
Here are the files if you'd like to use it: DOWNLOAD (480kB ZIP file).
This includes the LyX files, and a subdirectory with .tex LaTeX files if you prefer to hand code.
I have used texlive on Windows 7 and Linux (Ubuntu) with good results. It 'just works' if you install texlive with all options (minus the languages you don't need). Some spacing might need to be tweaked depending on the length of your thesis title. I am not a LaTeX expert, so please don't ask me detailed questions. I bluffed my way through this and got it working, and I've put it up in response to requests from my supervisor's other students.
My thesis has been accepted and is now available to view on QUT ePrints. Click here to go to its page.
There are two ways of managing fonts. The template currently uses the Libertine package to typset the document using Linux Libertine (serif) and Linux Biolinum (sans serif) typefaces. If you need to use unicode characters, comment out (or remove) the
line in QUT_Thesis.sty. You can then define your on serif, sans serif and typewriter fonts in LyX (and probably in LaTeX too, but that isn't something I did). You then compile/view the document with lualatex instead of pdflatex. If you do this you get all the nice features of ligatures too. If Linux Libertine is not your preferred font then you can specify your own OTF/TTF fonts or include another font package.
I have structured the thesis with separate files for each chapter. The 'master document' features in LyX mean that bibliographies specified in thesis.lyx are available in the sub-docs, provided you've defined the master.
Bibliographies & Citations
Bibtex is great for managing references. My preferred .bib editor is JabRef, which is a cross-platform JAVA application. I have used macros for journal and conference names so I can choose between 'short names' for journals publications (e.g. IEEE Trans. Indust. Electron.) and 'long names' for the thesis (e.g. IEEE Transactions on Industrial Electronics). It is just a matter of including the .bib file with the definitions in the master document. If you don't want this, just enter the full name of the publication in your .bib master.