Choosing the Right ones.  There is a smorgasbord of bike wheels out there.  How do you know which one is the best one for you to pick?  As with everything, there often is no right answer.  Check out the Wind & Rolling Resistance Archive for more info on what forces affect your bike as you roll down the road.

Trade-offs.  The basic gist of resistance forces is that there are trade-offs between aerodynamics and weight.  Improving aerodynamics often increases weight and rolling resistance.  One thing, however, that reduces air drag and weight, is reducing the amount of spokes.

On a bike wheel, the spokes at the top move faster than the spokes near the hub on the wheel.  This is easy to see because the out part of the wheel must cover a greater distance than the inner parts of the wheel, yet over the same period of time.  Additionally, smaller wheels must spin quicker to cover the same amount of distance as a larger wheel.  

Wheel size.  Wind tunnel tests have shown that a 650C (26-inch) wheel and a similarly designed 700C wheel have equivalent air drag.  Add on the extra stem length to compensate for the smaller wheel and you may actually have more air drag with a smaller wheel.  Also, because the smaller wheel must rotate faster to go the same speed as a larger wheel, the rolling resistance will also be higher.  So unless you are riding a small bike, stick with 700C sized wheels.

Weight.  Lighter is better as long as the quality remains high.  See Wind & Rolling Resistance Archive for more detail.

Air Pressure.  Keep them pumped up!  More is usually better, unless you are riding on really rough surfaces.  Again, see Wind & Rolling Resistance Archive for more detail.

Tread.   Smaller is faster.

Rim Depth and Spoke Count.  To make this easy, an increase in rim depth and a decrease in spoke count equates to more speed.  Wind tunnel tests show small improvement when rim depths are in the 30-45mm range, but when they hit 60mm, the benefits become large. 

Discs are the fastest wheels, but can wreak havoc when used on a front wheel.  A nice crosswind might just toss you in the ditch.  As a result, the best combo in a crosswind includes a super-deep (90mm rim depth) on the front.  When battling hills, head and tail winds, go for a 60mm wheel depth or three spoke wheels.

Paired-Spokes.  These rims have reduced spoke count which helps weight and aerodynamics.  These are good rims, but make sure the manufacturer kept the spokes as far apart as possible.  Bunching them together hurts aerodynamics.

Tires. Make sure the tires have a smooth transition from the tread to the casing.  A thick step between them can ruin the effects of a good wheel by disrupting proper air flow.  The tire should only be slightly narrower than the width of the rim.

As usual, there is a lot to consider with every component of your bike.  As conditions change, the ideal equipment changes.  If your budget limits your options, just go with one set that covers most conditions the best.  Your local bike guru should be able to set you up with what will work the best for your riding style and based on the types of races you will be doing.  Below are pics of some of the wheels we discussed above:

disc deep
shallow   tri spoke