1. First, I try to have paper and a writing utensil on my person at all times. One never knows when inspiration will strike, and I like to be ready to jot down or develop an idea when that happens. To that end, I generate a list of bullet point ideas for future reference.
2. Once I have an idea for an adventure, I use a technique that I stole from my brother Nick. It's a flowchart that starts with the adversary's actions, draws in the PCs, and then leads through various possible developments to what one hopes is a satisfying conclusion. This all keeps in mind, of course, that no GM plan ever survives contact with the players.
3. Sometimes--and especially for my recent Sixth Gun campaign, I've wanted to develop a location for use in a particular campaign setting. For that purpose I use a chart, one that has sections for different elements of that place. This helps me organize my plan for it.
4. Finally, during each session I use my notes to keep track of damage to various characters in battle, skill checks that characters make for later reference, possible repercussions for future sessions, and the like. Here's an example of that.