Wow, im actually surprised at the responses here...gedit to keep notes on something as large as a possible target (think corporation: various APs, IPs, domain names, people's names/emails/etc., passwords, possible relatioinships between all the above and other secondary targets) is kinda hard to keep straight in a simple notepad file...
d0xbase is nice and i love the retro feel, but if its a large target and i need to keep track of a lot I prefer Maltego (also from paterva, but with more capabilites) . It allows you to create a visual diagram of the investigation, akin to the FBI tracking boards you see in a movie with all the pushpins and photos and string connecting things, and each node (for lack of better word) can have additional info and notes appended to it. So at first glance you have an overall picture, then by clicking a node you get a more complete look at each individual portion of the current investigative project.
Sorry for the late response, i haven't been around much lately
