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Using the AF fine-tune command here in the Setup menu, I can refine my camera's understanding of a particular lens's optical characteristics. In other words, I can make it focus better with a very specific lens. Now in the real world, you really only going to notice the difference if you're working with a lens that can open to a very, very wide aperture, so a 2.8 lens or a 1.8, or faster. Anything that's slower than that, there's really no point in fine-tuning. Also, this fine-tuning process is pretty complicated.
You need some special gear to really do it well, and a company called Michael Tapes Design makes an excellent product called the LensAlign that's designed specifically for going through this particular process, so you probably want to invest in some of that hardware. You can find instructions on how to use this feature on page 338 on your manual. Note that it also does warn you that fine- tuning is not recommended in most situations and that it is possible to screw up your focus. Now, I've never actually messed up a lens.
I have, before, found through fine-tuning process that my lens needed some adjustment. I've done that and not really noticed any difference at all in my final results. So whether this is worth dealing with really depends on the type of shooting you do. If you do a lot of shooting at f1.2, and are finding that maybe your focus is a little bit off--more than you can compensate for with sharpening software--than you might want to take a look at this.
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