I have an excel file with several sheets. I have one sheet for respective topic: Swords, Clubs, Axes, Distance weapons, Magic spells, Blacksmithing recipes, Leather crafting recipes, quests, monsters, foods, armors, shields, boots, helmets etc. I keep a word document with different ingame languages. I have another Excel file with the roadmap.
All the sprites and tile sheets are in a folder. I also store the latest backup and version in the same folder.
I keep these files in my dropbox so I can switch between computers.