If I bought a set of road wheels made for an 9 or 10 speed cassette in the rear could I convert the back wheel to just a single fixed cog or even a flip/flop or would have have to get new hubs as well? The front wheels are interchangeable between fixed and geared no? I'm asking because of this set I found on Ebay. Looks like a nice set of wheels for good money, but not for fixies.
Mavic Open Pro Shimano Ultegra 6500 Wheel Set 700c Black Road Race Bike Wheels | eBay

The headache this will cause you will not be worth the few dollars saved. Keep it simple and just get a track wheelset.

I agree with this, which will not get you a cup of coffee, but just a thought.

Ok, but what about the front wheel? will any 700c front road wheel work as long as the spacing is correct?

Front will be fine. Road and track bikes both use 100mm spacing up front.

That's a pretty nice wheelset for a geared bike. I agree with the others though, get a fixed gear wheelset.

You can buy a New Set of Track Mavic Open Pro's with some Formula Sealed Hubs, for about $30 more shipped. It will also have a flip flop hub and you should be able to get it in rear spacing of 120, 126, and 130mm.