I used to use PBWiki (back when that was a thing, I guess - I think they've changed names?) because I liked the idea of having a wiki for my projects - but these days, I use a complex system of scribbly notebooks, even scribblier sketchbooks, a big folder on my computer labelled Grassblades (in which dwells an infinite number of subfolders within subfolders - it's subfolders all the way down), and an ever-growing word-document dubbed, and I'm not even joking, "Masahiro-plotnotes-FORREALSIES". It shares a subfolder with other documents named "Character-list", "Important-scenes", "Outline" and "Main plotpoints", because why keep one document to refer to when you can keep several?
But really, it lives mostly in my head.
I've toyed with the idea of getting a Pinterest-board to organise my visual references, but then I realise that no, I don't have to do that, because I've got a meticulously organised reference-library sitting right there on my harddrive - and backed up to my external harddrives. It is sorted by type (buildings, animals, costume, landscapes, textures, etc.,), further divided by type - or time-period, in the case of the costumes - and then further divided by specifics (The "Birds" folder divides into "Owls", "Corvids", "Passerines", etc., etc., and the Owl-folder is further divided into "Barn owls", "Horned owls", etc., etc.). Some pictures are even saved in multiple places - both in the big reference folder, and in the folder dedicated to the project I'm using it for, so that I don't have to go digging through an entire library when I'm working on a specific project.
I am my very own librarian.