I'm kind of organized?
I have a website for my toy collections (MLP, Neopets, and various dolls) that I used to be really on top of updating. I still have a record of most ponies I own including a picture and when/how I got them organized by generation. Since donating a lot of G3s and G4s I need to update who I still have, as well as take new pictures when I get a new camera, but overall its still pretty accurate. I haven't gotten many new ponies (or dolls) since I stopped updating it.
As for storage, that's a whole different beast. When I moved out in early April my boyfriend put my ponies in a one of those big plastic tubs that can fit a ton of ponies standing up. Whatever fit in there, I took. He just put them in completely at random and I did very little to interfere with that. They're almost all still in there, although the lid has been open and just resting on top for months. No tissue paper or anything. However I do at least know where all of my ponies are. Only a few aren't in that tub and I know exactly where they are.
My dolls, on the other hand, are a disaster. Some are out, some are in specific boxes, and some are god knows where. Its a total mess. Trying to find a specific one is almost impossible.