My master of science thesis
Source is made with emacs org-mode and exported to LaTeX, but don't worry, it is readable on any editor! org-mode just helps me on organizing stuff. Pictures are made with ditaa(in ASCII) and rendered with Java. Rendered pictures and pdfs are included.
Commenting to source can be done either on .org or .tex, but .tex gets overwritten so easily.
In .org, comment starts in first column "# " (hash space), use it for commenting, perhaps with your own initial like
# RI: this needs some explanation