1) Test Turrets for repeatability,
I hang a measuring tape to ensure it is vertical then I set the rifle up at 50m so I can see the finest measurement lines on the measuring tape. With the scope perfectly level I adjust the scope from one extreme to the other watching the reticle move, many scopes do not move the reticle in the last few clicks of the top of their travel so make sure you know that the click is actually moving the erector cell. Mark the tape where you started and where you finished and take that distance and divide it by the number of clicks it took to get there. To get your 100m equivalent you will have to multiply your result by 2x. Example 48" of travel *2 = 96" at 100 yards now divide this by the number of clicks, say 417 clicks and that give you a click value of 0.23" per click. My S&B 3-20x PMII has click values of 1.03cm not 1cm btw. This is some of the closest I have seen. Once you know what your click value really is then just plug it into your ballistic computer and your headache is gone.

2) Measure actual click value of your scopes elevation and windage adjustments
Using the same tape measure run your turrets all the way up and down multiple times to their extremes to ensure that they return to the same spot on the tape measure. Do this for windage too, this is like the box test that many do at the range but the box test does not give a precise result because rifle faults and inaccuracies can give inaccurate results.
3) Verify that the crosshair is square with your turrets. This is simple hang a rope, a line, or a tape measure like I do for the other tests. Now level your scope "perfectly" now your reticle should be perfectly vertical with your reference line you hung.
4) Test Parallax adjustment for faults
Test parallax at all distances to ensure your reticle doesn't move off zero while adjustments are being made, This is a major flaw found in most US scopes that nobody knows about. So when your ballistic computer isn't tracking what your scope is using to make hits this is likely the problem. Every Nightforce I have tested has this issue, the reticle will move 5+ MOA of vertical during the entire parallax adjustment range!! S&B has minor movement when adjusting parallax below 50 meters but that is so close that it really isn't an issue.
5) Test magnification range to again ensure that the reticle position doesn't move off zero when you adjust the zoom. I haven't seen a high-end scope have this problem but on a African hunt last year then the crappy guide rifle we had to shoot had a trashco scope on it and it most definitely moved the crosshair when we changes the zoom.
6) Resolution, brightness and other lens tests.
Bet you thought I was going to have a very scientific method of testing this, I don't but at 50meters if I can resolve 1/16 inch lines on a tape measure I am happy, and on the range if I can see bullet impacts at extreme distances clearly or holes in paper at 500 yards (assuming mirage permits) then I'm happy. As far as brightness I like looking through scopes side by side but the best testing is the range test.
7) Almost forgot my final test. If the scope is longer than your rifle and as heavy as your rifle, then you didn't buy a scope you bought a baseball bat and you need to take up a different sport.

Now go test your scopes and don't yell at me when you find any issues with them because many of you will. You get what you pay for and you don't really even know what that means sometimes, ultimately it means frustration on the range and lost of wasted practice because you can't discern where discrepancies are coming from between your ballistic calculator and actual firing results.