It's funny. When +Vincent Florio , +Glen Hallstrom and I go through prepping for the next episode of The Brainstorm Podcast, I probably do less prep than the other two do. Or at least, less written down prep.
My commutes to and from work are usually filled with listening to assorted gaming podcasts and thinking gaming thoughts. When it comes to prepping for the next podcast, I spend part of that commuting time brainstorming ideas and answers to the next topic we will be discussing.
I use much the same process when I prep for a sandbox styled game session. The main difference is, after the brainstorming for a game session. I write more than just a few words down jar the memory - I go with a sentence or two - sometimes even more, as I may be doing this a week or more in advance. For podcast prep, much of it is done the same day, so the thoughts are fresh and don't need much to jar them lose.
While I like the idea of a "DM's Binder", I couldn't even keep colored index cards in any semblance of order. These days I use a 5x8 notebook in chronological order - doesn't matter whether I'm DMing or running a PC, my notes go in chronological order. Yeah, maybe my advice isn't the advice to follow... heh.
I always go for rulings over rules to keep the session's pace moving. Nothing sucks more than a 10 minute library search to look up some obscure rule. Wrong ruling plus pacing plus immersion plus fun is infinitely better than right ruling minus pacing minus immersion plus frustration.
(as future episodes of The Brainstorm Podcast are released I'll be expanding upon my thoughts in a series of posts here at The Tavern)