I registered both at Babies 'R' Us and Buy Buy Baby. While the former has just about anything you'd need, the latter carries higher end brands,offers more of an assortment, and a more extensive collection within the major brands. I have only shopped at the Buy Buy Baby store located on Central Avenue, Scarsdale, New York and my experiences have been only great.
While the registry is imperfect - items become discontinued quite often and not all things online are available in-store, I would recommend this store.
They have the best stroller selection and are so well organized, in general, that everything becomes so appealing. On numerous occasions I've purchased small items that I really didn't need, but had to have.
I love both stores for different reasons. But the reason I return to Buy Buy Baby is it's interesting selection of goods.