I don't like the unfinished look of the palettes when people use white stickies on the inside of their palette lids to identify what the colors are. I know I'm really picky, and I like everything to look perfect.
For me, after I depotted my shadows I used a hair dryer to heat of the label on the bottom of the eye shadow pot, and then I peeled it off, cut out the name & texture from the big round label and stuck it on the bottom of the magnet that I had attatched to the shadow pan. After I peeled the labels off, they were still sticky enought that i could just stick them to the magnet without having to use any glue or anything. All my shadows are like this, and if I'm really dying to know the color I'm using all I have to do is lift up the pan and check underneath. It's really not that big a deal. I know most of the colors off the top of my head anyways.
It's kind of hard to see with the lighting, but you can see how I stuck the black MAC label onto the magnet. It's much more professional looking & closer to how MAC sells their pan shadows.
How I organize my palettes: Color coordinated. I actually have 3 now, so the order has changed a bit, but you get the idea. I like it, cuz I know one palletes has all pinks, purples, etc, and the other browns, greys & greens.