Definitely old school "on paper" organization here. A computer was only used to write up and print out the various player handouts.
I used lots of 3x5 cards for things like NPCs, ships, rumors, mooks, businesses, locations, etc. I had a slush pile for each and one fish out a card whenever necessary. Once a card was used, I'd pop it into the campaign folder with either penciled notes on it or another 3x5 card with notes attached by a paperclip to it.
The way my 3x5 card system worked was fairly simple. Let's say it's my
Active Duty IISS campaign and the players are "chumming" for general information. They work the street successfully and come up with a "small-R" rumor; that is a rumor which is used just to set a sense of place or provide some general scenery. I pull out a rumor and a NPC from their respective slush piles, roleplay "Pete the Finn" mentioning that he's heard several tramp captains' grousing that the orbital fuel boss off Conway is demanding larger bribes, and then paperclip the two cards together with a third on which I note the "where & when" of the encounter. From then on during the rest of the campaign every time the players visit that particular system I know, and hopefully the players remember, that Pete is there as a possible encounter and source of information. Each time the players met Pete, I'd update the "where & when" card.
A "big-R" rumor, that is a rumor which was a plot point or critical piece of information was handled differently. In those cases, the rumor and/or the NPC weren't simply plucked out of the slush pile. They were crafted well beforehand when the adventure/session was put together. Once again, the information and the source were on two separate cards paperclipped together.
As each 3x5 card bundle was produced, I'd pop them into location folders. Places important to the campaign had individual folders while less important locations shared folders. A location folder would contain maps, background write-ups of varying detail for my own information, and a "what, where, & when" log sheet to keep track of events.
The "what, where, & when" logs also allowed me to prepare
Our Story So Far..." handouts when there had been too much time between sessions. A quick half-page precis usually got everyone back up to speed neatly even after months.
To keep track of a campaign's plot and various subplots, I'd use graph paper to sketch a industrial production or
Gannt chart of sorts. Using a simple example here, imagine you're planning on making a pancake by a certain time. You know you'll need a certain amount of flour, milk, and eggs all by a certain time, that the mixing will take a certain amount of time, that the griddle will need to be a certain temperature by a certain time, and that the cake will need to cook for a certain amount of time. The pancake is the plot, the flour, milk, and eggs are the plot's requirements, the griddle is another requirement with its own sub-requirement of heating, and finally the mixing and cooking is the plot taking place.
You can see that some of the requirements, like the flour, milk, and eggs, can arrive in any order. Another requirement, the griddle, can only take place once several other requirements have already occurred. Finally, the plot itself will occur after the requirements are met, in a certain time and place, and then for only a certain period.
Now, take my goofy pancake example and apply it to a bank robbery. You've got requirements like getting weapons, scouting locations, obtaining a getaway car, and many others. Some requirements can be done in any order, some can only be done after others are complete, and all must be achieved before the robbery occurs at a specific time and place for a specific period.
These plot production or Gannt charts allowed me to keep track of what was happening away from the players' actual location, when certain events had to occur, what events could be allowed to slide, and how everything was supposed to some together. Because I knew what had to occur, when it had to occur, and how everything fit together, I could easily juggle the players' activities while adapting my plot to their actions on the fly.
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Now I have printed "equipment cards" that I give to my players when they find or create something new. (I also have blank cards that I can hastily scrawl on and give to the players if I don't have the necessary card - by next time we play I prepare those in print).
