An obvious and pretty conservative choice for titles would be Gill Sans (or, if you're feeling fancier, this: http://www.myfonts.com/fonts/k-type/gill-new-antique/).
In the same vein, maybe also Cabin could work.

As for monospaced fonts, there are several that could fit the bill (Anonymous, Droid Mono, Inconsolata, Consolas...) you should start with the one you're using for actual programming and see how well it prints out.

1) What's the thesis about, specifically?
2) How long is the text?
3) What are the nature and frequency of the illustrations?
4) Why did you choose Joanna?

For a monospaced font, you might choose a design by
somebody who is both a programmer and a type designer:
http://levien.com/type/myfonts/inconsolata.html
But the questions above come first.

hhp

One of my favourite magazines used to set code snippets in Letter Gothic, a 12-pitch face.

1. One for titles (Serif or Sans-Serif)
2. A Serif for the body (I've chosen Joanna by E. Gill)
3. A monospaced typeface for the portions of code

Could use something like Fedra Family from Typotheque. Has serif, sans and mono.