It's the thickness of the gasket. 1 hole is the thinnest, working up past 2 and 3 before arriving at no holes being the thickest. You are supposed to measure the highest protruding cylinder with the head off, and then once you have found the highest one, you select your gasket:
Protrusion 0.50 to 0.60 mm - select gasket with 1 identification hole.
Protrusion 0.61 to 0.70 mm - select gasket with 2 identification holes.
Protrusion 0.71 to 0.80 mm - select gasket with 3 identification holes.
Protrusion 0.81 to 0.90 mm - select gasket with 0 identification holes.
"It doesn't swoop, curve, or look like it's going fast when it's parked. It never looks like it's going fast. It doesn't go fast
." - Richard Hammond, BBC Top Gear