Sounds like you have flat spotted or dented your rim. it is out of true radially. You can try to identify the low spot, loosen the spokes in that area and try to push or pull the low spot out of the rim.

Here is a thread about ways to fix a flat spot. http://www.bikeforums.net/showthread...-spot-on-a-rim

Or you could take the rim to a bike shop and have them verify that the rim is bent and see if they can true it up.