My inventory is organized into Hats, Tops, Bottoms, Shoes, etc and then in those categories, the EIs, REIs, CIs, CS items comes before the common sets (The higher end items are also arrange according to it's price, so the more costly items are always first). The items in each set, is also arrange in a rainbow fashion- The white being first in the set, red second, orange third (And so forth) and black being last. I know it sounds pretty confusing, but it's not!
Here's a screenshot of the first two pages, so you can see what I mean.
Initially, it took me about two days to organize my then inventory of around 2500-3000 items (Now it's...a lot more). It was first organized in merely colours (In a rainbow), but it got so large that I couldn't use that anymore- I then decided to reorganize them, in a way that's closer to Tektek, so it'd be easier for me to put outfits together (It was also because I had to move accounts, I didn't want to pay 100k for a username change -SHOT-) Anyway, I wasn't used to it at first, but I slowly got used to my new inventory. It's been awhile now since then (Two years ago, in fact), and I think that this is the best method of organization for myself. All the new items I get, I organize them into my sets right away. Makes getting used to the location of the item easier.