Which Garamond?

If you're going for this traditional look, you should probably use a slightly heavier version of Garamond (or similar old-style) for the footnotes. Sometimes called an "optical" size.

Garamond Premier Pro is Adobe's latest version of the venerable style, and comes with "optical" sizes, as well as all the characters you would probably require for a thesis (including "true" superior figures for references).

Once you get the page format laid out in such a face, then you can consider a titling font: it may be the Display optical font of Garamond, or something quite different -- maybe even a bold sans, which could also be used for subheadings.

Thanks Nick Shinn, that is helpful - I'll see if I can get these fonts somewhere.

@ Christopher Dean, my thesis is basically about hormone signalling in plants after they perceive a herbivore. Effectively plant biology, with a bit of analytical chemistry and biology mixed in.
If it would be any help, I can try to post a picture of a chapter title page and a normal page of what I have now?

However, the university I graduate has no requirements whatsoever for the thesis (only the content).
I don't really like to mix a lot of fonts in a doc, but everything the same is a bit boring too.
The only thing about style I've ever learned is that mixing sans-serif with serif is a no-no, but don't even know if that is true anymore...

… mixing sans-serif with serif is a no-no, but don't even know if that is true anymore...

Nonono. This has never been true. Using a sans as a complementary font for serif bodytext is common practice. It all comes only down to the question: *which* sans?
You may do a search for “humanistic sans”, e.g. on MyFonts.com. You can make the site display all fonts found with a test word like “Hamburgefonst”. Take some time to look at it. You’ll notice that some sans faces owe certain aspects of their aesthetics to faces like Garamond - and therefor may fit the bill.

I agree with RadioB. Syntax is a good choice for you. It pairs very well with Garamond and is humanistic which is appropriate for your context.

Actually, I discovered that my institution had the full Adobe package, so I've changed the font to garamond adobe pro (12pt), because it has ligatures.
As headings I now have garamond adobe pro in small caps, in 'caption' style, which looks alright, subheadings are garamond italic, 14pt.

I might go for either something very frivolous for the headings (on the left page there's 'chapter 1' and on the right page there is 'Running Title'), or for a Sans-serif.

I guess I won't use geometrical margins as I don't know how to correct for the printing margin and they take up a hideous amount of space.

Anyway, cheers for all the help - I'll probably have some stupid questions later...

Thanks for all the suggestions, this is what I've finally come up with, and I'd love to hear some feedback.
The main text is garamond premiere pro, 12pt. The abstract is the semibold version, the italic heading is garamond italic, and the subtitles are hoefler text - Ornaments (no idea how I came to this, I tried different things and I liked this)
I chose the normal garamond italic because it looks nice, and it is different from the garamond pp italic, which I have to use regularly in the text to for species names, gene names, etc.

The title is garamond pp caption, small caps.

Let me know what you think
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The purpose of small caps and old style figures is to lessen the visual overemphasis of words which must be set in all caps, and of numbers, especially years. As you have set them here, the HAMPS jump right off the page immediately. Could you try setting the acronyms in small caps, and the figures old style? That is the traditional way of working with a Garamond in text.

The colour of the page as a whole is good.

Cheers for the suggestions, my professor wants indents at the beginning of a paragraph, and it'd be silly to upset him - I can make them a bit smaller though.

Small caps for the all caps abbreviations is a very good idea!

Whle I agree that this looks a bit busy here, is this exceptional - there are only a few instances (two or three) in the whole thesis where the subheadings are followed directly by a paragraph heading - in this instance I even added it myself (the 'introduction' heading isn't in the thesis), because this was the only page with all the styles on one page.

I prefer one lead as it is more salient than an em. I do not use Microsoft products so I do not know how this is achieved in Word.

If the text is set 12/18 (font size is 12, paragraph "line spacing" set to "exactly" 18pt), then you set "special" "first line" "by" "18 pt" instead of ".5 in".