I'll confess. I'm pretty compulsive about how I organize my pins, too. I have a plastic container that holds all my keepers from Japan. There's another plastic container that has my trading pins from Japan. I usually keep these two boxes on the dining room table. All of my best traders are currently on two plates in the china cabinet and the pins I'm holding to trade with my friend in Japan are all together on a shelf in my office. Swamp Fox has a separate page for pins that he's not sure where they belong -- I use a similar system, I have two cardboard boxes in my office that hold pins I'm not sure where they belong.
I do have some of my keepers in a book -- carefully arranged by however I happened to pick them up when I found a few minutes to "organize" them.
If you think I'm kidding, ask my daughter -- she'll tell you I'm not. This is actually where my pins are at the current time. I organize my photographs the same way -- my wedding pictures from 36 years ago right next to a picture of my granddaughter playing on the slide.
Oddly enough, this system actually works for me, and I could tell you where any of my pins are at any time (well, most of the time) And I do actually have two sets of pins framed in a manner that would make sense to most people, one of Tokyo pins and one of my favorite year 2000 pins. I'm not sure how that happened!