As I've been learning the ropes here at Socialtext, one of the the tools I use the most, and it may seem to be slightly silly, is the sticky note utility in the Applications folder on my MacBookPro. Why this particular options? I like it because it gives me a place to stash ideas quickly, order them quickly, and if I need to reboot my system or close out the app, I don't have to remind myself to save every single time. It does all that for me, because I can be stupid some times.
I typically use it to keep a little narrow strip column and keep it up in the corner at all times. Additionally, I use what I call "heat mapping" to make sure that things I need to focus on immediately catch my attention (red text, blue text, green text, bolding, etc.) so that I can look at the given areas. Are there other more sophisticated tools that can do similar things? Sure there are, but my goal is to try to find tools and methods that don't get in my way. Also, it's important to keep each "heat map" area small. Since we have an extensive document management system, often I need to condense these cheats into larger documents that others can use, and by the time I've gone through and massaged the cheats to a reliable knowledge state, then I can offload them into HOWTO guides and such for others to use and play with.
Sometimes we over-think our tools. We want so many neat bells and whistles, and often, they get in the way of what we really need to do. Often, the simplest approach that lets us accomplish our goals is far superior to the comprehensive but cumbersome tools that we often use. I thought it was a corny little tool at first, but I've grown to love its for its bare basic abilities and how I can create as many as I need. It's also a lot nicer than my old approach which was to actually put lots of post-it notes on my monitor (hey, it stood me in good stead for years ;) ).