As Darth said,how bad are they? Wheels do go out of true,esp machine build stock ones. I've had no issues with the same wheels on my Novato. Also,how much do you weigh? If you're well over 200lbs,you might want to look into some heavy-duty wheels.
MTB wheels are commonplace,and very sturdy,but they also tend to be pretty wide and won't always fit skinny street tires properly(one of the worst tire experiences I ever had was putting 1.3" slicks on a set of Rhynolites).
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C'dale BBU('05 and '09)/Super Six/Hooligan8and 3,Kona Dew Deluxe,Novara Buzz/Safari,Surly Big Dummy,Marin Pt Reyes,Giant Defy 1,Schwinn DBX SuperSport,Dahon Speed Pro TT,Brompton S6L/S2E-X