I'm currently doing research for my Master's degree. One of the biggest headaches is keeping it all organised. I have several notebooks full of notes from my reading. I have dozens of links to policy documents, speeches, and news reports online. I am constantly inventing structures for my writing, and re-inventing and re-shuffling. I am in desperate need of some kind of filing system.
One thing I often notice is the overlap between education and gaming. For instance, this recent article about designing a gaming space has a lot of similarities with how teachers try to design their classrooms. So it occurred to me that the solution I've found for organising my research could help with my upcoming campaing. (I say "upcoming..." It depends on player apathy!) I've found two free (hooray!) mind-mapping tools: XMind and Personal Brain.
XMind allows you to create rather traditional mind-maps: a central topic with sub-points coming off. My favourite feature is the ability to hyperlink either to files on your computer or to web sites, which helps me organise my links thematically. There are plenty of keyboard shortcuts so after a bit of practice the interface is a breeze. XMind is best suited for hierarchical data, because its diagrams all assume that the parent-child relationship is the most important for your information. This mind-map is an interesting demonstration of the format. I use it for my research (central topic, subdivided into schools of thought, again subdivided into researchers, with subtopics to take notes on my reading). Because it is hierarchical, it would really be most useful for game notes that are also hierarchical: maps in mind-map form (divided into regions, smaller areas, and individual places), hierarchical organisations in your campaign world, or a campaign structure (divide into adventures, encounters, NPCs...).
Also a mind-mapping program, but one I found immediately more useful for gaming (and less useful for my research). Personal Brain allows you to establish information hierarchies, but it also lets you create information that cuts across those relationships. Check out some of the samples to see what I mean. When you view your data, you look at one item at a time and things that are within one or two relationships of it. I've found this amazing for developing a campaign setting. My central topic is my city, divided into people and places. Under "people" I have little hierarchies described (most of the organisations in my city are hierarchical), and under "places" a list of sites in the city. The city also links to rival cities in the region, useful for long-term campaign development (eventually these cities can develop their own internal mind-maps). However, because you're not as restricted in how you describe relationships (any datum may have as many links, horizontal or vertical, as you like), it's better for describing a dynamic city. Within every hierarchy I've tried to create relationships that go across to different organisations (so some priest has a rival in the count's court, or one of the council members has a brother in the priesthood...). This makes the world feel less disconnected, and if I use my laptop at the gaming table (it's small, so I think I will), it's easy to situate any NPC in the grander setting. Another fun trick is putting the party in as a part of the mind-map so I can track the allies and enemies they make and how that entangles them in politics. The biggest downside about PersonalBrain, however, is the inability to visualise ALL of your data at once. I like it because you can establish the relationships between details, but if you want "big picture" software, go for XMind. (Or both!)