The Zipp 404 consistently get incredibly good reviews, but in all fairness I've never ridden them. But when I see independent review sites consistently rate them best in class it's tough to ignore.
I have a set of Reynolds Aero 46 wheels that I was able to get for a ridiculously low price from my LBS - and yes they're a Reynolds dealer. It ended up being an end-of-model-year set that the distributor wanted to get rid of and they offered to sell them for $1000 off street price (not MSRP, street price). It was too good to pass up. So, the wheels actually came from the distributor and weren't sitting on-hand at the bike shop.
That said, I'm VERY happy with the Reynolds wheels and I wouldn't hesitate to recommend them. Reynolds also has their RAP program, and while it costs extra, it has to be one of the best deals out there. You can google it, but basically it is a no questions asked replacement program. Hit a curb and break the wheel? Replaced. Get mad and hit your wheels with a hammer? Replaced. You get the idea. With any luck I'll never have to use the program but it gives me great piece of mind knowing it's there.