This is for battery calibration. Basically there's a sensor in your phone that is used by your phone to tell how full/empty the battery is.
This sensor doesn't actually know how full your battery is, all it knows is how much power is coming from your battery at the time. The problem it has is that all batteries are slightly different, and their capacity goes down over time and usage (a three year old battery will not be able to hold as much charge as a brand new battery).
Your phone keeps a record of the maximum power it's ever had from the battery, as well as knowing the minimum power that it can safely work with before it has to turn itself off. It uses the difference between those two numbers, and the current power at any time to calculate how much percentage of your battery you have left at that time. So with a new battery, the phone might be telling you that the battery is fully charged because it's charged to the highest level the phone's ever seen, but if you leave it charging a bit longer then it might charge more, and then the phone can recalibrate itself and use this new value as the most it's ever seen.
You should only need to do this "over-charging" with a brand new phone/battery, after that the phone know the maximum values, and can more accurately tell you when it's full.
