Micro-Adjusting focus of lenses is tedious and imperfect. A number of commercial products exist to help calibrate lenses but only to validate and check focus. Because these products are disconnected from the camera, they cannot do anything to set the micro-adjustments. On top of that, micro-adjustments are incapable of characterizing variations in focus according to focus-distance and focal-length.
Well, there can be a better way, at least for modern DSLRs and Sony SLT-series. Even better, it could probably be implemented via a firmware update. All that is needed is a camera with both Phase-Detect and Contrast-Detect autofocus. Almost all DSLRs with Live-View can do this now. SLDs, other than those using a translucent mirror cannot but they do NOT suffer from that problem anyway.
The key is understanding the nature of the problem. A contrast-detect system evaluates focus directly from the imaging-sensor, therefore always has the correct focus when it manages to lock. A phase-detect system uses a dedicated AF sensor and that one can be slightly off compared to the actual focus distance. A focus micro-adjustment is simply an offset from the focus measured by the phase-detect AF sensor.
A camera that supports both types of autofocus can therefore simply measure the offset itself. It can do so at various focus distanced and even focal-lengths by instructing the user to move the target or change the focal-length. To ensure accuracy, one would have to use a special focus target, either provided as a solid object or printed from a supplied PDF file. The firmware necessary to do the adjust would basically instruct the user how to place the focus target, perform measurements and repeat this a few times for each lens. It would then be able to characterize and set focus micro-adjustment curves that follow focus and focal-length variations.
Hopefully we can see this solution implemented soon by at least one DSLR manufacturer. Since service centers often perform micro-adjustment and those have to be repeated each time the camera body gets upgraded, it is in their best interest to provide such a self-service solution.
While we wait for self-adjusting cameras there is a detailed explanation of how to do this manually at the Photography StackExchange site.