I don't think "well-organized" is the way I would describe it. My basic organizational system is: grab a part, toss it on a shelf. Looking closer I do see that I've got all the tires, all the handlebars and all the saddles on the same shelf. That was only semi-intentional. There are also small parts scattered across my garage that haven't made their way to a shelf yet.

Accumulation is the key. Most of this stuff came from used bikes that I needlessly upgraded. When I first started over-upgrading bikes I kept the original parts with the idea that I'd put them back on if/when I decided to sell the bike. Eventually I accumulated enough stuff to build a complete bike from a frame. Now I just never get rid of anything that might eventually be useful.