I’ve started a thesis, these are my toys:
Bazaar (yeah, the new one, I’m not that crazy…) for version control. As you might expect, the distributed element is a wee bit of overkill, but not as much as you might think. It makes backups easy.
LaTeX and BibTeX. I’m not a complete LaTeX purist; I find it’s more trouble than it’s worth for shorter documents, or at least, it has been since office suites on Linux started being easily installable and usable for me. (I recall, for example, in 2001, when Abiword exported to PDF but did not export the paper orientation with it. Since I’ve never owned a printer, export to a portable format for printing has always been my feature of choice.) But for a 200+ page thesis, it’s better than the alternatives, because it doesn’t involve typing XML tags and it is text based and therefore can be version controlled without custom proprietary tools and recovered by hand. And it’s designed for academic papers.
I’m not so enamored with BibTeX because I find it’s an easy format to get wrong. I suppose I should at least try EndNote someday so that I speak the same language as my librarians, but even if it is as good as everyone claims, it takes a lot to get me to switch operating system. (I have, in fact, only done it twice: DOS 2 to Windows 3.1 to Linux.) I probably should play around with BibTeX frontends again. Last time I tried pybliographer it was missing some useful features, although now I can’t recall what.
Tomboy for note-taking. This is my real discovery of the past month or so. I like wikis for notetaking in principle (hyperlinkiness is next to godliness) but in practice I find that the press edit, wait, edit, press preview, wait, edit, press preview, wait, edit, press save, wait cycle is too slow for comfort on a web connection. They’re also not really well designed for the task of taking notes into several pages simultaneously, or bouncing between them. So, I ran apt-cache search wiki specifically in search of the wiki idea implemented as a desktop program and Tomboy is what I found. I’ll be curious to see how their ability to interface with other programs goes. If it looks attractive I might try and hook it up to one of the BibTeX frontends I’m yet to find.