I keep what is essentially a lab logbook next my work desk. The natural chronological order works mostly well: (1) notes on related topics are often close in time (the temporal locality, in a way) and (2) it helps to find "stuff I was working on two months ago", or "right after I finished that project in May".

Also, I noticed I prefer writing on separate sheets better than a notebook. This way I can take several sheets from different time periods and work with them as a single group. When I am done, sorting them back is easy as long as each sheet is marked with the day it was originally worked on.