Car batteries are not designed to be completely discharged, they are designed to provide short bursts of high energy (e.g. to start an engine), they have relatively thin (compared to deep cycle batteries) plates and a high plate count to provide high current for short time intervals.
As a battery ages (and is repeatedly discharged and charged, e.g., by starting and running your car) it goes through a process called sulfation, the lead in the battery sulfate is converted (a little at a time) to a stable crystalline form that no longer dissolves on recharging ultimately reducing battery capacity to the point where it will not crank your engine over. A complete discharge of any lead acid battery will result in some breakdown (sulfation) of the plates in the battery and reduce its life; because the plates are thinner in car batteries a complete discharge will reduce battery life or completely kill a battery a few years old. Sulfation also increases the internal resistance of a battery reducing charge efficiency and increases the rate of battery decline.
After charging your battery you should expect it’s voltage to drop to 12.7 to 12.6 volts fairly quickly since this is the normal open circuit (load) output voltage on a fully charged lead acid battery. Under no load conditions it should hold close to that voltage (within 0.1 volts) for 24 hours. An open circuit battery voltage of between 12.2 to 12.3 volts indicates 50% charge. At 12.0 volts I consider a lead acid battery to be dead! (Note to check the no load voltage on your batter you need to disconnect it from your car.)
Personally if your battery is 3 years or older and has been completely discharged I would replace it. It is simply a dead battery waiting to happen.
Have Fun in your Pcar - Martin