I'm using a basic set of handbuilt wheels for just about eveything - Open Pro CD rims with an Ultegra 6700 front hub and Powertap rear. The Powertap was used, so I've got about a grand in them; they'd be ~$400 with standard hubs. The main disadvantage with these wheels is weight - they weigh ~2,000 grams. By using different hubs, you can reduce the weight by over 500 grams. I know Eric has had problems with Open Pro rims, but I've been lucky so far. Another traditional rim with no history of problems that I'm aware of is the DT Swiss RR465 - same weight and price range as the Open Pros. I've got a set of them built with Ultegra hubs and have had no problems, and they're pretty sweet.
If I were to get a wheelset right now and weren't worried about training with power, I'd get a set built with relatively light hubs and either Velocity A23 rims or, if I were flush, HED C2 rims. If I were worried about training with power, I'd get a set of the Powertap training wheels for about a grand. I wouldn't worry about aero wheels unless I had lots of descents or could hold at least the low 20s mph on solo rides.
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Regards,
Chuck
Demain, on roule!