Try not to do that again. I killed both my PowerBook G4's battery and my MacBook's battery by running out of juice and then forgetting to charge them for a day or so. When I got around to trying to charge them, the computer wouldn't recognize the battery.
The same dang thing happened to my bro's MacBook battery too!
Basically, there has to be enough power for the battery's control unit to work, and if it manages to get too low (like, you run the computer down to the point that it won't even turn on AT ALL), then after some time there won't even be enough power for the control unit, and unless the control unit has power, it won't let the battery charge.