I love taxonomy. Not as an abstract method to make purely academic distinctions, but as a useful tool to group like items. Taxonomy is everywhere, and when it is good you don’t even notice it, but it makes life easier. I also have a three year old, and I love him more than anything. He even restores his toys when he is done playing with them, so I very rarely step on a Lego. But he can only restore toys which have a known place, so we do a lot of taxonomy exercises in the playroom.
We have shelves, drawers, hooks and bins. Hats and superhero masks go on the hooks, costumes in the drawers. Bins can contain all one type of toy (like Legos) or a mix of types that share a theme or get played with together (like Toy Story). The wall of shelves has 5 columns, and 4-5 rows. A column might contain similar items, like Cars, Trucks, things that go, as well as related books, standing up next to a bin of small trucks. (And I might read a story about dumptrucks to him while he drives around and loads on with blocks.) But puzzles all stay grouped together even if they have a transportation theme, because the boxed puzzles stack neatly, and the flat wood puzzles all fit in a unit where they can slide into a rack. (Plus, we don’t use them together while driving trucks, and he does not like to be read to while working on a puzzle, we talk about how the pieces fit instead.) The top shelves are for toys which need supervision, like the RC helicopter, or would not be safe if we have younger kids visiting, like beads and Magnetix, plus things we would use together like board games and a globe.
Everything on the lower shelves he can use without help. We rotate things more or less seasonally, because things seem new after they have been packed away in the closet for a couple of months. We also keep a basket filled with small rugs which he uses to define his space when he is working on the floor, and some trays for working with small things at the table.
Knowing the rules for what you are working with goes a long way. Taxonomy supports findability. Even a three year old can restore his toys when they are organized based on the way he uses them.