"Centering" is not actually the problem, but "aligment". The distance from the hub to any of the dropouts is defined by the specific dimension of the bearings, cones, spacers and locknut used in each side of the axle, none of this is changed when opening or closing a quick release skewer. The "mobile" parts of a skewer squeeze the frame from the outside (outer sides of the droppouts), but the inner part of the dropouts directly press against the locknut in the axle.
This, in conjunction with vertical dropouts virtually eliminates any chance of installing a rear wheel badly aligned. The only thing to worry about is to properly seat the axle in every dropout, taking it as far into the dropout as it naturally goes. This type of frame only allows to attach the axle in one position, thus as long as you do it reasonably right, the wheel will be centered and aligned.
A frame with horizontal dropouts however pose a bit of a challenge. Again, it is not the centering of the wheel, but its aligment what is difficult. If your frame has perfectly simmetric dropouts, a good strategy is to install the wheel with the axle in the deepest part of the dropout, and adjust brakes and deraileur in this position. This way every time you have to re install the wheel, simply put it as deep as possible.
If this is not an alternative, a set of stopper bolts may do the trick. Alternatively you can use paint or stickers to mark aproppriate aligment marks to help you during the task.
In the case that you use disc brakes, they are a pretty reliable way of assuring the wheel is propperly positioned because they have very tight tolerances. Before removal, check that the disc is centered in the caliper and that neither pad rubs it. When you reinstal, check the same.
As other answers state, bad wheel alignemt is a big issue with rim brakes. This makes them a good indicator too. If you have your brakes propperly tunes, the pads land in the center of the rim's braking surface, and when you release the lever, they should "rise" more or less the same distance from the rim, so, perform this check after attaching the wheel and most likely you'll be fine.