I use the third line. Just for fun, I once checked exhaust clearance with the center mark and with the right mark. There was no difference. The valves stay fully closed (where they have to be to check clearance) for more of the crank rotation than is shown by those three marks. It is CAM chain timing that is much more sensitive.
Make sure you are close to TDC on the compression stroke by putting your finger over the spark plug hole and start looking for the marks when you feel pressure building. Also, always re-check clearance after you fully torque the lock nut.
Sorry, I should be more precise: Both VALVES may stay closed longer than the radial marks indicate, but the CLEARANCE varies from zero to whatever the maximum clearance is before adjustment (which is at TDC). So as you rotate the crank, clearance goes from zero to a certain value and back to zero. I've never actually checked at what point before, during, and after the radial marks this happens. I only checked the exhaust valve clearance at both the middle and the right mark and found no difference.
In earlier engines the right hand mark is a T.