My first principle of organization has four divisions according to use: 1) reading, 2) study, 3) art and 4) collection. These are not "forever" categories. There's quite a bit of overlap and I frequently switch decks, especially between the first two which together number less than 20 decks most of the time. I also keep these close at hand in baskets, on tables and desks and in my carry-all.
The third bunch are decks that I love for their beauty and sometimes for their usefullness as well. Some I read with, but not consistently. Some I don't read with for various reasons, but I gain a lot of insight just by looking at them. This is quite a large group, easily the largest of the four, and is housed in a series of small trunks--small so that I can find the deck I want when I want it. Also, I sort this group according to their format (Marseille, Thoth, RWS, Etiella, Mincheates, Majors only, Oracles and Other) and within the RWS category, by publisher.
Last are decks that I keep as part of my collection. These are kept in their original boxes and are housed in a small bookcase and in a couple medium sized drawers. It's perhaps double the size of the first two groups. About half of these are where they are because they are difficult to keep. They're oversized or in book format or the packageing is integral with the deck, etc. The rest are there because besides being rare and out of print, they aren't decks that I consult very often though I do appreciate having them.
Sometimes I'll select a subject--say decks featuring cats or Egyptian tarots or versions of RWS or decks by Caroline Smith--and pull them out of wherever they are. Scattered on a table, they reveal things they might otherwise not. And it's fun, for me and for whomever happens upon them. But I don't organize this way. Too complicated.