To prepare for this, many GMs use various means of organizing the information. Online works well, but even then I find I prefer a physical binder. It's easier to flip through a binder at the table than go searching through my G-Drive or some other online cloud service.
Lately I've been meaning to re-organize my binder. I am thinking of the following sections, and am posting it here because it might be of use to others. Also, maybe someone will have a crazy good idea that I need to hear and will share it in the comments.
I like having a place, at the front of the binder, to keep the PC's character sheets. This keeps the sheets with the game and means that as long as I remember to bring the binders, everyone will have their character sheet. It also lets me review characters during preparation. It's no good making a situation hinge on a particular set of skills or spells if no one has them - even if I think they're obvious good choices. Finally, I can also use this section to keep cheat sheets for magic items and other custom stuff.
In my current binder this section is called 'Maps' but I want to change it. I want to change it because I often need more information than just a map. Maps are great, they give you a visual, but written information makes the map more. I can have a map of a city, or I can have a map and a write up for the city. This puts context to the picture and explains what I'm looking at.
A location section should also have sub-sections for any major locations. A grouping of maps and write ups for a big city, while another place may only have one map and a few scribbled notes on things.
The beauty of this is it can be as detailed or not as needed. If I have an area well planned out, I can have computer generated maps and typed up write ups. On the other hand, if the PCs end up in a village that I have to make up on the fly, and all I have is a quick hand sketch map for the general shape of the village and a couple hand written notes about what the PCs did there, that can be put into the section and developed later, or just kept as is in case the PCs need to go back.
Previous Sessions' Notes
A place for notes from the past several sessions is always useful. This lets you flip back if something needs to be referenced or if you just need a reminder for what is going on. I'd recommend keeping at least all the information for the current arc in this section, but the previous arc may also be good. Obviously, once older than that these notes can be kept elsewhere (or summarized and disposed of.) But it's always good to have a record of the last few sessions. Even if just to help prepare the next few.
Blank Lined/Graphing paper
You have to take notes on something, and graphing paper can double for quick maps in a pinch. Enough said?
In D&D the Monster Manual can be a royal PITA to juggle when you have an encounter with several monster types. Even worse if one monster is in the default Monster Manual, one is in Volo's Guide, and the others are in Mordekainen's. I do have the Deck of Many Monsters box sets from Deck of Many, but they don't have everything covered. So often I'll end up with print outs of sheets from the book, or of Copy and Pastes of the stat blocks. These are handy to keep track of because monsters can be reused - sometimes reskinned but same stats - and why print it out again and again?
I like to keep master lists of NPCs. I normally do these in Google Sheets because it lets me have a master list, a list for each PC, and a list for other big items in the game all derived from that master list (spreadsheets are magic, you can't convince me otherwise.) At the very least I like to track
Notes gives me a place to write any quirks or other specific things (i.e. if a PC owes them money or something). Having this information easily at hand can be a life saver for finding who that NPC was that time in that place. At present I have near 100 tracked named NPCs for one of my D&D games. The other has a lot less but it's been running for a lot less time, and well, I've killed a lot of NPCs in that game.
Having some variant of this - or at least notes for major/plot worthy NPCs in the binder is also good. For the Queen of a close country I have a whole page write up on her and her personality. I reference it often, and she has come up a lot in the last few arcs, so it's been good to have it in hand.