A nice wheelset is the best upgrade you can make on your bike, if you ask me. Shell out a few bucks and get something sweet. Are you riding fixed or SS?
Bicyclewheels.com has some pretty good deals on wheels made out of good-quality components.
Or, you could find some hubs that you like and match them to some rims that you like and get them built. I had my Miche Primatos laced to Velocity deep-Vs at Urbane 3 years ago and they haven't gone out of true yet. I am about 190lbs or so and I am pretty rough on my wheels and, now that I think about it, I am amazed that they haven't needed a truing yet....weird.