I have a script that simply touches a file with filename <timestamp> in a directory and cracks it open in vi. I hashtag things in the files so I can grep them later, and keep all the files in a private repo on github. I used to be about pen and paper, but after filling out eighteen moleskins with semi-useful info in them, keeping them in a searchable format on the computer starts to make a lot more sense.

For actually remembering information, note taking is a good first step, but I usually don't keep those notes. To actually assimilate knowledge you've got to to take it in, put it in the context of the rest of your knowledge, contrast it with other things, and ultimately use it to produce something.