It has two meanings that I know of.
One (and by far the most common) refers to the money that you have spent yourself, versus money that comes from another source.
If I travel for work, and the company pays for my plane ticket and hotel, but I have to pay for my meals myself, I spend that money "out of pocket" and get paid back for them later.
Or you buy some items that you plan to resell. You spend 50 dollars on them, but you only sell 40 dollars worth. That's ten dollars you are "out of pocket."
The other meaning I have only heard recently, and is used at work to mean that someone is unavailable. Sometimes people travel but still have their cell phones and access to e-mail, but sometimes they are "out of pocket." If you are on the airplane, for example, you are out of pocket.