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My favorite for this is Clear Duct Tape. Put down one piece of tape, write on it with your permanent marker, and put another layer on top of it. You don't have to worry about the ink rubbing off and if you change what's in it you can swap tape easily.

I've personally found paint pens to work quite well. You can find them at Wal-Mart in the craft section and most likely any craft store. They are the brand "Painters" made by Elmer's. I use the ones with fine tips for labeling, which is slightly more defined than a Sharpie. They also come in a variety of colors so you could even color code different ...

I occasionally have to label smooth plastic surfaces around the office that get handled regularly. As you say, even a sharpie mark wears off after a while. What I do is to write the label with a sharpie, then put a piece of tape over it. Don't use the clear "scotch" tape, but the more permanent milky kind. Make sure it is well stuck down with no air ...