The short answer is that you don't want to run batteries below 3.0V ever, and ideally want to avoid large current draw below 3.5V. For a 3S battery, once you start seeing voltages in single digits (3.33V/cell is 10V, below that), it's time to land as a quick reference point - although you can set more precise values of around 10.6V as the warning point through telemetry at a transmitter and/or OSD on an FPV display.
The real issue you're trying to avoid here is that in the Lithium-CobaltOxide (LiPO battery chemistry), below 3.0 volts (can be 2.8V or so in Li-Ion batteries), the battery starts plating lithium permanently onto the anode reducing the capacity and discharge performance of the pack. Doing this greatly harms the battery, so avoid that at all costs.
The reason I reference the 3.5V point is that typically you have another 10% of battery capacity left in order to affect a safe landing approach pattern without being under time pressure to land quickly, and make a good safe landing - also under load, the battery that is at 3.5V in flight will tend to recover to 3.7-3.85V depending on craft and setup, which is more appropriate for storing a battery as you travel back home to the bench charge the battery to its proper storage voltage (3.8V).