First and foremost, I have no affiliation with the FoCal software or developer, so this truly is an unbiased assessment.
Lots of users here claim that all they need is a real life target and a tripod to determine the best microadjust (MA) values for any given lens. I used to make the same claims, but in reality, there is a lot of guess work involved in that method. I'm not saying that you can't get good results, but it does require precise methods and a very good eye to determine maximal sharpness. Even with the LensAlign Pro equipment (which I am selling for anyone interested), it can be extremely difficult to determine which adjustment is sharper than the next.
A few months ago I broke down and purchased the Focal Pro software...best purchase I've made in quite awhile. The software helped me figure out that I had a malfunctioning 70-200II and 50 1.4. The 70-200II had been in my possession for almost 10months and using other methods, I could never get it to perform quite right. It always seemed as though the AF was inconsistent. Using the MA process and focus consistency with FoCal, I finally had a way to objectively analyze its performance. Sent it to Canon and they also confirmed that it was malfunctioning. Came back from them and is now FLAWLESS. Same with the 50 1.4. My main point is that it can be difficult to tease out tease out these problems without using some form of an objective measurement. Our eyes tend to fail at distinguishing minor and sometimes major differences in sharpness.
My latest experience with this software has been just as magnificent. I calibrated my 2.0X TC with my 70-200II....WOW. I was actually quite pleased with the sharpness prior to calibration, but now I'm thrilled. I was willing to sell the 2.0X a few weeks ago because I just didn't use it very much, but I had a definite change of heart after seeing what it can produce in combination with the 70-200.
Moral of the story: Take the guess work out of microadjusting and buy the FoCal software. If you've spent thousands on your camera and multiple lens, you owe it to yourself to get the most out of the equipment.