It has been more than I decade since I used paper notes—everything is on the wiki now—but my system is pretty sound. I hope that you find this useful.
Requirements: Manilla folders, stapler, paper clips, writing utensils, post-it notes, loose unruled paper.
Generally:
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If there are multiple note papers on a topic, they are paper-clipped together and a label is written on a post-it that is stuck on the front of it.
For the GM:
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PCs folder—contains all the notes for each PC in the game.
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NPCs folder—all the notes about NPCs.
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Current folder—this has all of the notes that may come up in the current system.
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A page that lists all of the locations in the campaign
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A page that lists all of the NPCs in the campaign
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A page that has a short summary of the campaign
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A page that has a list of open questions/quests
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Archive folder—this has all the of notes that were previously in Current, grouped logically.
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(optional) Faction and Monster folders. Varies by campaign.
For the players:
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A folder for each PC that has the canonical character sheet and printouts of all relevant rules for the character (spells, feats, etc.) Also any notes that the player wants to keep, as well as handouts.