It depends on what you're trying to accomplish.
AMA Supersport roadracing bikes are set up with bearing clearances on the very outside of the spec. This results in minimum drag, and therefore increased horsepower output, at the cost of reduced engine life.
Along the same lines, you'd set up other clearances (deck height, wrist pin-to-piston crown dimensions, etc.) to maximize compression ratio. A lot of these are done by the factory because they have a whole production line of parts to check. As part of QC on the production line, they check the dimensions of new parts. It's a simple matter to pick out the pistons with the tallest wrist pin bore to piston crown height and set them aside as race pistons. These will give slightly higher compression ratios than pistons on the other end of the tolerance spec. You can do the same by picking camshafts with lift values on the high side of tolerance, rods on the long side of tolerance, etc. They don't mean much individually, but when you add them all up together it results in a stronger engine. That's why the factory bikes are always faster than the privateers; they have access to a LOT more parts to choose from and also have no problem with an engine that only lasts one weekend because the bearing clearances are loose.
I've also heard of folks surface grinding valve shims so they can set valve clearance specifications to the absolute minimum, which also gives you maximum lift and duration with that camshaft.