A "29er wheel" is a 700c rim that takes a wider/larger tire. A "29er frame" and fork have sufficient clearance for the larger tire and the geometry is adjusted to account for the larger wheels/tires. What you need to look at is the type of tires, wheels and bike you want based on the conditions you ride in.

Since I have many routes to choose from for my commute depending on weather conditions and my mood, I use a 26" disc wheels with 1.5" slicks for mixed use riding (dirt trail/paved MUP/road). I also have studded 26" tires for winter riding. On the same bike, I run Mavic Speedcity 700c disc wheels with narrow road tires (23/25mm) for "all road" commuting. The weight savings of the lighter road tires and innertubes of about 800 grams and lower rolling resistance provides a small increase in speed (around 1-2 mph).

The 700c wheels with road tires are almost the same overall size as the 26" wheels with slicks, so there is no problem changing wheels. Of course, this only applies since they are both disc wheels. Rim brake wheels are more difficult to swap out given that the braking surfaces are in different locations on a 700c vs. 26".

I have no desire to use heavier 29er wheels with heavier 29er tires. One area I don't want extra weight is in the wheels. Look at the specs and add up all of the weights (wheels, tires, innertubes) and you will see that there is a significant weight penalty in the 29er wheels. Personally, I think 29ers for commuting are slower and less efficient, but for some reason they are becoming increasingly popular.

I'd like to hear from 29er commuters to see if they have a benefit I am unaware of, other than just "they look better" or "they seem to roll faster."