I've organized all my memes by alphabetical order so my folder of ponies goes under "P"
There I separate everything by mood as I primarily use these as reaction images. So "Action," "Angry/Annoyed/Bored," "Cute/Wholesome," "Happy," "Horror," "Humorous," "Interested," "NSFW," "Otherwise /mlpol/," "Relaxed," "Sad," and "Surprised/Anxious/Sad"
Each of this is subdivided for every major character in the series + Anonfilly, Aryanne and Co. and Leslie Fair. Pictures with more than one pony or a minor character/OC are lumped into "Other/Multiple" while those about non-pony creatures are put under "Non-ponies"
"Action" is instead divided into "Art," "Dramatic Poses," "Informative," "Non-MLP in MLP," "Regular Activities," "Sports," and "War and Politics." "Art" contains separate folders for animation, synthwave aesthetics, music (whether an actual music video or a picture of ponies playing music), and traditional art, nature and landscapes. "Dramatic poses" are what you'd expect like ponies dressed up like superheroes. Informative means art references and theories about the show. "Non-MLP in MLP" includes folders of crossovers, ponified concepts and people, posters & logos, robots/computers, and space. "Regular activities" has folders of day-to-day pony behaviors such as bathing, celebrating, eating and drinking, working out, flying, wearing costumes, playing, going to school or romance. "Seasonal" has pictures of holiday-themed pictures grouped by holiday. Sports has pictures of ponies playing different sorts of sports. "War & Politics" has folders of ponies fighting, propaganda pieces and soldiers or ponies with guns.
/mlpol/ has folders for /mlpol/ memes, /mlpol/ logos and posters, /mlpol/-themed propaganda, posts I've screencapped, and /mlpol/-themed videos.
My technique involves a lot of nesting to stay organized and although I've thought about a tag-based system the advantage of folder nesting is its compatibility with different operating systems.