I've wrote my Bachelor thesis in LyX and it's awesome, especially for math!
If someone is interested (it's about Bitcoin and in German), here's the source: http://www.math.uni-bremen.de/~jhasse/Bachelor-Arbeit.zip And here's the PDF: http://www.math.uni-bremen.de/~jhasse/Kryptografische%20Grun... Nothing fancy like Clean Thesis though. I like the http://motherfuckingwebsite.com/ approach better ;)