Many bicycles, old or new, have original factory-equipment wheels that are mediocre at best. Fancy names on your parts are of little benefit if your wheels are constantly going out of true, breaking spokes, or flexing too much under load. On the other hand, a nice, well-built wheel set tends to give the bicycle a high-quality feel and inspires confidence.
Building bicycle wheels is a craft. The fundamental process can be taught in a few hours - it isn't magic or an "art" - but it takes hundreds of wheelbuilds, perhaps, before the process is internalized. It starts to feel like instinct, but I use technological tools, like spoke-tension meters, to keep myself honest. The result of this combination of experience and technology is a dependable set of wheels that will last, with minimal maintenance and adjustment, until your brake pads wear through the rims after tens of thousands of hard miles.
Aside from the obvious quality advantages of good handbuilt wheels, another reason to order a custom wheelset is to match the appropriate rim and hub to your needs. Often, we have needs for something just a little weird, and we can't buy it off the shelf. Need a generator wheel with 40 spokes? Want to try a 650B fixed-gear? How about putting nice new rims on your 1972 10-speed bike with 120 mm hub spacing? You simply can't order the appropriate wheels from QBP or anywhere else. They have to be made-to-order.
I use a wide variety of hubs and rims that I feel are sufficiently high-quality. I tend to shy away from hubs and rims that have a proprietary design that limits inter-compatibility or future serviceability. I use Wheelsmith stainless spokes, primarily because Wheelsmith spokes are available to me through my usual sources in bulk quantities at reasonable prices, and because Wheelsmith spokes have always impressed me with their quality and consistency. I usually recommend 14g spokes (2.0 mm thickness), but when it's desirable to save a little weight I will use 14/15g double-butted (thinner 1.8 mm center section) spokes, which cost a little more. Wheelsmith spokes and nipples are available in shiny silver or black. Black costs more.
I use a variety of rims and hubs, but have a few favorites that I use again and again. Scroll down to the wheel packages sections for details of some of my favorite combinations.