First, let's face it-there are any number of ways you could do this.
But after years of fighting a mess of resistors in a Plano box and looking up the color codes with an online calculator whenever I needed a specific value I didn't know off the top of my head I finally went through and did this last night:
This works well if your collection is in that 500-1000 piece range (sold in odd configurations at RadioShack and several online houses) and you already have a setup that is dependent on plastic cases like this one-say a tool-box style carrier or a slide out shelf of them. I did roughly the same thing with caps/semiconductors/small hardware/misc parts, but those tended to be easier to sort by size. Resistors not so much. (I do like the three-ring binder full of buisness card holders idea, but I had committed to this already when I saw that.)
What really sets this organization apart for me is the division method. Ever since I was 12, when reading resistor codes it was always that third band that threw me off. It turns out that for a plastic case like the one in the photo, it's the third band that makes it easy to organize them. About 7-8 divisions is perfect-and there are only 8 possibilities for band 3 on E12/E24s (the 5 bands still f me up-I say screw them.) So dividing things into 1-9.1Ω, 10-91Ω, 100-910Ω, etc. works pretty well. (I put the 10M ones in with the 1-9Ms because why dedicate one compartment to a single value?) The extra compartments work for CdS cells, panel-mount pots, wire-wounds, etc.
Further, I found that you don't necessarily have to use a pemanent ("Sharpie") style marker to color code the wells. "Crayola" brand water marker dyes seem to be holding up just fine. Of course there isn't a "Gold" one of those, but that's easy enough to remember.
Also, just so I know I'm not getting my reads wrong, I put this chart on the hood:
It's nice to have when it's late and your eyes and brain are tired.