Each party has their own notebook and time related things go in there. I have a column of timestamps just so I know what time and day it is in the dungeon and I can make notes here related to things like how far ahead they’ve paid for their inn state (I’ll note what date it expires).
Dungeon-specific stuff go in a dungeon-specific place. This means stickies (like “This guard is dead”) in the module if paper, or in an outline file if digital.
Town and island stuff go in the A7 box. Rumors and treasure maps and rival groups. Every time I get (or make) a new module, the rumors and hooks that lead into it need to go in here.
Players keep track of their characters own stuff. This is such a life-saver for me and I would’ve gotten totally burnt out if it weren’t for them. For things they don’t fully know what it is, like mysterious keys and weird potions or items, we assign a code, something like “Key SoC23-M” that remind me where I can read more about that item and its properties. (It’s often a reference to what book & part of that book something is from.)
Domain game stuff and also locations of dungeons and islands go on my huge Inkscape file that has like 30 layers.
The player-facing equivalent go on our wiki.
House rules and scheduling go on our wiki. Random tables and DM-facing tools go in my A4 accordion file, which can also house printouts for home-made modules.