The quality comes from being hand built by someone who takes pride in their work. Not machine built, or sweat-shop assembled. The same spoke/hub/rim combination will last longer and require less maintenance if it has consistent and adequate spoke tension and starts out properly trued.

That said, the vast majority of machine built wheels are good enough, and you probably won't notice the difference until you've been riding them for several years. A lot depends on the price difference. I learned to build my own wheels, more for the fun than anything, but also because it's cheaper. Paying someone else to hand build a wheel may or may not be an efficient use of money, depending on what you put your bike through.