[pjc50]

The best tool for this may be a paper notebook. Especially if you interleave it with something like the "pomodoro" 25 minute work units. Then spend a few minutes writing down what you did and what you expect to look at next, what unsolved problems you have, etc. before going back to the computer.

(I tend to do this at work with Notepad, but in the past I've found the medium shift to pen and paper useful in itself for changing mode of thought)

[PaulHoule]

I use Microsoft OneNote for this. Searchability is fine, but if you write down the context of what you are working on, you can save minutes to hours picking up where you left off.