I have three large dressers that hold the majority of it. One dresser is strictly MAC products, which are then organized by type (blush, lipstick, gloss) and alphabetized by letter (but not within letter, it’s just all As, Bs together, etc.). One dresser is for very high-end/luxury brands. One dresser is for mid-to-high-end brands. I use Helmers in a closet to store brands that I only have a few products of (regardless of price point) as well as drugstore products. I typically organize within drawers by brand, product type. I use plastic pins to hold palettes (Urban Decay palettes are separated out), MAC palettes are stacked on shelves in a closet along with other freestyle palettes (Anastasia, Makeup Geek, MUFE, and so forth). Nail polish I keep in Helmers.
For those who aren’t familiar with the concept, project pan typically involves using up products you already own – e.g. you have to finish your foundation or five lipglosses before buy more of that type of product. Much like a low or no-buy, it can be set-up however works for your stash, but the premise is really to encourage you use to use things you already own. I have not!