When looking for wheels for my fixed cross bike I was told that on a 17mm rim (track wheels), I could run up to a 32c tire without worry of rolling or pinchflatting. On the 29er wheels, IIRC, I could run down to a 28. I wanted to run 38c's so I went 29er.

So long as you were looking for a larger tire, a 29er wheel should work fine.

-Rob.