I’m mostly running games online these days, so I don’t have a GM toolbox so much as a GM desk.
On the screen is Roll20 with the player-facing map with their notes written on it, and Discord, which we use for voice and text chat. The microphone, audio interface, and headphones (not shown) are all related to that. All the character sheets are on Roll20 as well. I do keep OneNote open on a second desktop, but that’s mostly for keeping track of stuff outside of sessions.
I have the PDFs for Stonehell, but I like running it from a binder, where I can make notes on the pages, and stick in sheets of loose-leaf paper with updates based on whatever the players get up to down there. It’s also handy having it all in a physical binder for the rare occasions when I run an in-person session.
I keep some time tracker sheets that I made in the binder as well, which I use to keep track of things like torch usage and wandering monster checks, as well as make notes about where the party was each turn and any interesting things that happened. I used to use the extra space at the bottom to note which player characters (it’s open table, so that varies each week) and hirelings were involved, and what monsters / treasures they slayed / liberated, so I can tally up XP at the end, but I recently started tracking that on a separate index card.
I keep some dice handy, because while Roll20 has adequate dice rolling commands, I like the psychological effect of rolling them on the table so the players can hear when I’m making a check (or just rolling randomly to mess with them). It’s the little things that bring a GM joy.
I don’t often look at the rule book during play, but sometimes it’s unavoidable. I really like the OSE Rules Tome for that, because it’s a nice size, and the organization and layout are as close to perfection as I’ve seen in an RPG book.