Rather than repeating stuff that others repeatedly repeated, I’ll just list some useful and interesting links about how to write your thesis (or just another paper) with LaTeX. This list will probably steadily be extended.
- VERY basic approach to writing a BASIC thesis. Also still uses only BibTeX.
- Good overview over the whole process of writing a PhD thesis. This one is especially notable for the General Thesis Writing Advice in the back.
- BibLaTeX/Biber and BibSonomy (yeah, that’s mine.)
- A pretty general list of packages.
- Really useful (and unknown to me) packages for writing a big, long thesis.
- Very interesting command for nested includes.
- The todonotes package!  I know that it has been mentioned in some of the pages above, but I cannot stress enough how useful this package is, especially for a long document!
- Resources for designing beautiful tables of content.
(Not compatible with the memoir document class! See http://tex.stackexchange.com/questions/33012/about-memoir-and-titlesec-incompatibility)
- More resources for nice part, chapter and section headers
- Some handy settings for partial building in TeXlipse
- Want to print nicely formatted matrices? Fancy some brackets inside that matrix?