Perhaps its my background in Mathematics, but I have a bit of a problem with the idea of 'putting thinking time on my schedule'.
I find that the thoughts come along when they want to and think themselves anyway. They laugh at my (paper) diary. I suspect that this is related to me being on the 'maker' schedule rather than the 'manager' schedule.
I really enjoy actual paper notes as well - particularly when you end up in creative thinking mode, having a completely non-technical capture medium does the trick for me. I've tried a lot of the electronic stuff, but plain A6 cards that I can later organize work wonders and I have yet to find something better (it's not really like I'm looking for something, though - I have found my sweet spot).
I find that the thoughts come along when they want to and think themselves anyway. They laugh at my (paper) diary. I suspect that this is related to me being on the 'maker' schedule rather than the 'manager' schedule.
http://www.paulgraham.com/makersschedule.html