Just bought a refurb ATV3 and received it the other day. It comes in a White Apple TV box that says "Apple Certified Refurbished" on the top. Identical to the retail box except for the different labeling. But yes, it is a noticeable difference in packaging.
BTW: IMHO buying refurb from Apple is a no-brainer. You get the same warranty as if you were buying brand new, but you are paying less and not drawing on more resources to churn out yet another electronics unit (i.e.: good for environment, even if negligibly so). Do it!