Andrew nobly pointed out a thesis template from UCLA that is very handy but not terribly well documented. I have eventually got set up and realised that the reference formatting in the text is somewhat bizarre. I have now switched back to abbrv until I find out what the UCT standard is. You will also need to add the amsmath and graphicx packages
A really helpful resource is Andy Robert's LaTeX Starter Guide which contains nearly everything you'll need to do maths, tables, figures and formatting. It even includes a comprehensive list of symbols so people like Raoul don't have to search all day for the infinity symbol :P
Editor-wise I am writing in TexShop, a Mac program and using BibDesk to store my Bibtex references. If you're in Windows I'm told that MiKTeX is very nice including a file structure sidebar and JabRef for reference editing. For those of you who break out in hives at the thought of learning a new markup language, try LyX, I've heard wonderful feedback about it.

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I'm using the same tools to write my thesis (Texshop and BibDesk and the UCLAthes template all on a mac). I have also found some weirdness regarding how it handles the Bibtex citations. For instance, I am using the agu (American Geophysical Union) style files (agu.bst, which you can get from AGU's website). These produce great Author-year citations when used with the AGU paper templates, but when used with this UCLAthes template, the citations look very strange: author, year, then the first three authors all just in the citation. And the reference in the bibliography looks odd as well. Would you mind letting me know if you've found a way around this? Thanks and happy writing!
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