I have a three-step system. In-game, detailed notes, and overviews.
Here's how I do it. I run a lot of games (5 pretty regular ones), so I had to get efficient
Using 3x5 sticky notes and notepads, I track happenings in the game - things that I thought up along the way, and things that changed during play due to player interaction. Some of these go into folders that I gather up once a month and...
I take those notes and enter them into documents and spreadsheets on my network using folders for world, kingdom, subdivision (duchy, et al), and important personalities/locations/etc...
I then summarize the games (every few weeks) in the website for that world.
The website is general, public info, the network holds the detailed info, and the notes get thrown away or filed in a folder somewhere. Though these days I rarely go back to folders.
I don't know if a similar system could help you, but it works pretty well for me.