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I've mentioned this a few times on /bant/ before, but I organize my files in an extremely rigid format, almost obsessively.
Folder structure is the most important part of organizing your files effectively, no matter how well you name your files it will eventually become bloated if you don't have enough folders. Personally I have one main folder that contains everything, and over 100 sub-folders within that. For anime I find that having a folder for each show works quite well, and if they become bloated then making a folder for each individual character inside that anime's folder works well. Other things I like to break down by general topic; I have a folder for screencaps that itself is broken down into more specialized folders like GETs, and bans. Finding a balance between having enough folders to prevent bloat, but not so many that each folder only has a couple of images is key.
I do filenames really simply, everything is in lower case, with a decent description of what the image is about as the name. For anime screenshots/reaction images I use <character name> <emotion> as a general formula. This works really well for me, but I built this folder from scratch after losing my last one, which was a mess. It could be a monumental task to build this kind of system from a preexisting folder, especially if it has 100,00 images.
