Do refurbished Macs come in the standard boxes when ordered from the online store?
Speaking from experience I can tell you that they do not come in the retail packaging. There are instead shipped in whitebox packaging.
My Mac was delivered by UPS, it was just the white box, with the handle, on the side of the box was the barcodes and address etc, there was a mention of Apple on the barcode stickers, but no Apple logos, or images.
The standard iMac box, I also know from experience has an image of the iMac on the outside and is a thinner box, (I'm guessing as it doesn't need to be shipped)it also has a gloss finish whereas a refurb box has a matt finish.
I also recieved a KeyBoard and mouse with my refurbished Mac and the internal box with these in had
on the exterior.
I ordered a refurbished MBP from the online store (early 2011 model) and it came in generic packaging. However, there was an OEM box inside the outer carton that contained the manual, re-install disc, and power adapter.
In terms of resale, which is why I'm assuming you're asking, you won't get as much without an OEM outer box.