I run Mavic Speedcity 700c wheels and Mavic Crosstrail 26" wheels on my MTB commuter, usually part of the week on each. In the warmer months, I have Conti Gatorskins 23 mm on the 700c and Conti Sport Contact 1.6" slicks on the 26". In the winter, Conti 4 Seasons 28mm on the 700c and Schwalbe Marathon Winter studded on the 26". Both wheelsets have disc hubs, so there is no issue changing wheels. I set up the fenders just above the 700c tires, so there is a somewhat larger gap with the 26" tires.

The 700c wheels with skinny tires are definitely faster on pavement and climb much faster, and the 26" with slicks are faster on packed dirt and gravel (probably just because I'm willing to push them harder). There is better traction with the wider 26" tires, so I use them when rain is expected or if my route will take me off the pavement. There is also a lower center of gravity with the 26" wheels, which is better when the conditions are bad. Comfort level is about the same for both on pavement, but the 26" are better on the trails.

Having two wheelsets is almost like having two different bikes. I love having the option to go with a road setup or a trail setup with minimal effort. In about 2 minutes, I can swap the wheels and am on my way. The downside is that each wheelset will run you about $500 when you add in the cost of tires, tubes, rotors, and cassette.