I like J.Stockard's website because it shows availability of items. They're great to deal with, and they've supported PAFF events - very generously, I might add. Same with Kevin Compton at Performance Flies.
Will plug Bob Mariotts. Blue Quill is good too and free shipping.
Problem is, when making an order it drives me nuts that a given place will have absolutely all but one critical thing I'm looking for. I'll say that just did an order with Bob Mariotts and it was the first place I've ever gone to online that had every obscure thing I wanted in stock at once. Seemingly every color/pattern option available for a given product.