How to manage theorist's "labbook"? Question:

Are there any guidelines, sources, or examples of good practices for maintaining theorist's research notebook?

Motivation and context:

Maintaining a lab notebook is a much advised (if not a vital) tool for doing research. Many do that nowadays also in electronic form. While the methods for writing and maintaining a labbook might differ in details, in "dirty-hands" (no offense!) experimental, or field disciplines, the basics are relatively straightforward and clear. The advice tends to boil down to keep a labbook per single topic one works on and then record all the experiments and thoughts related to those experiments into the notebook. Simplifying a lot, in the end, the researcher (team) would compile a paper from the notes in the notebook.

Now situation of a researcher in a more theoretical discipline is strikingly different. Usually one engages in research on several topics at the same time. The problems a researcher works on are often intertwined and one's view on them changes over time, often merging originally separate streams of thought into a single one, or vice-versa. The work revolves not around experiments which would have a clear objective, but rather around currently prepared papers and then "a cloud of ideas". In summary, theorist's workstyle tends to be very non-linear. Maintaining some kind of a notebook is still a good thing, if for nothing else, then for not forgetting about stuff. My question is about how to go about doing it.

I am after a practical tool helping me to archive my thought process for long-term, as well as efficiently manage and keep an overview of the evolution of the several interacting topics I engage in.
(Supplementing F'x's answer.)

Physical notebook

I use it all the time, as it is the quickest way to write mathematics and jot diagrams. It's low tech, so it's "always on" (e.g. I cannot run out of batteries). 

I have one A4 notebook (so I take it anywhere), with removable pages.

I try to devote a single page only to a single project. On each page I note 3 things:


date,
title (or, actually, a pictogram) of the project,
"page number" for pages on the same project in a given day.


After some time (could be the same day, could be never) I take off pages, to fit them into thematic folders (and usually throwing away most of things, because they are "non-recyclable" rubbish; if it is "recyclable" then I scrap the important things, writing them on a new page).

However, such operation has trade-offs:


(+) sorted by topic,
(+) higher valuable content density,
(+) can be viewed "all at once" by putting pages on a desktop,
(-) I cannot take all of them anymore,
(-) it's somehow easier to loose it, unsort, or torn/coffee split/... it.


Electronic notes

Electronic content is much more linkable, searchable, easier to share, more polished etc. However, it takes much more time to write formulas or draw diagrams.

Different things work for different people, but some kind of personal wiki (or a well-organized text file system) seems to work the best.

I'm not settled down, but I'm switching from TiddlyWiki (very neat but requires a browser to run) to Gitit (so I can write in Markdown, with LaTeX inclusions, in any text editor).

I tried Evernote as well (and I'm using it for other content) but for highly-linked content it does not work for me.

See also:


How do you keep your research notes organized? - MathOverflow
Is there any efficient non-linear note-taking software?
Software/App for electronic research notebooks