Center to center (often abbreviated C-T-C) is used, as the moderator said. The reason is that sights control bullet launch angle. This is usually measured in minutes of angle on adjustable sights. This angle is subtended by a width at the target which grows with distance (one MOA is about 1.047 inches of target width at 100 yards, 2.094 inches at 200 yards, and so on). The bullet diameter does not grow with distance, so there is no way to make angle-controlling sights account for bullet diameter at different distances. Sights can only account for where the bullet points, as determined by the center line of the bore. This is also where the center of the bullet is when it exits the muzzle. Also, by using center-to-center, two shooters with different caliber weapons can still compare accuracy in absolute terms when comparing group sizes. Perfectly accurate shooting, after all, is when a bullet goes where you pointed its center using the sights, and not off to one side or the other of that.
The confusion can come from how you make the measurement? It is hard to exactly see where the hole center is, so a common technique is to measure the outside edges of the two holes farthest apart, then subtract one bullet diameter to get the C-T-C number. The caution here is that sometimes the exact placement of the edge of the hole can also be uncertain. Look for the dark mark left by the bullet.
There are various target shooter's aids to help find hole centers. If you explore the web sights that cater to target shooting, you will find them (Sinclair International, O.K. Webber, Champion Shooter's Supply, Champion's Choice, Russ Haydon, etcetera). I'll leave it to you to Google their URL's up. I find the clear plastic with hole outlines printed on them are easiest to use at the range. The plug style may be more accurate, but you are not allowed to have one with you at the range.
Nick