There's a ton of ways to do this. Some prefer not to organize their pastels at all but keep them all in a can of rice flour and just root for colors. I think that's a great method, but I'm too anal for that. Sigh :P
I use a total of 6 different brands that range from .38 to .55" in diameter (Rowney and Sennelier to Schmincke and Unison). Because I prefer to arrange mine by color, I'm currently using 2 three-drawer and 3 two-drawer wooden pastel cabinets to store them in.
They are arranged by color family -- for instance, once of my drawers starts with burnt umbers and then goes into the other warm colors in that range, gold ochres, brown ochres, etc., the next drawer holds the raw umbers and moves on to the rest of the cool colors. After color, I have them usually arranged by brand, however my favorite tints and shades take precedence and I keep them at the front of each group.
The pastel cabinets aren't that pricey (to me). The three-drawer ones are about $25 on sale and they hold about 72 pastels in each drawer (depending on the size) for a total of about 216. Unison and Schimcke pastels *just* barely fit in the drawers. I have to be careful when I close them :P I wish they made these just a little bit deeper.
I really like having the ability to look at my piece and thinking, "okay, warm brown animal", and pulling out my warm brown colors and putting them on my desk :P
That's just one method, and I'm sure interested in hearing what systems others here use, too!
<FONT face="Script MT Bold"><FONT COLOR="#AB4835"><FONT size="5">Roan</FONT s></FONT c></FONT f>
<FONT COLOR="#8A1010">Nan dèanadh mo làmh mar a dh'iarradh mo shùil!</FONT c>
-- <FONT size="1">If my hand could do as my eye would desire!</FONT s>
<-- pastel open stock vendor sources & reviews!