A second is a board that has a cosmetic blemish. It meets 100% of the quality standards as far as manufacturing goes, but didn't make it out of the paint booth perfect.
I have a custom second, and I swear to you, I can't find anything wrong with it. I almost think they sent me a first by mistake. Seems kinda silly, but for the people that are paying full retail, they want their boards perfect.
I bought a 08 Custom X second for 50% off, and I searched high and low for the error and could not find it. The only evidence of it being a second was where they stamped "Second" on the front tip of the board, and the fact that I was not (as) poor after I bought it.