I'm surprised to read of the scuffs someone mentioned above. Most items would have the casing replaced. I would return one if it had any physical flaws. Of course, I see brand new Apple devices with tiny flaws, so anything is possible.
I agree the box is a bit of a let down. Refurbished iPads at least still come in a nice white box, whereas the Macs just come in a white shipping box, so the box you see at the door is it, not a second box inside.
For me, the biggest reason not to get a refurbished unit from Apple: the pricing isn't that good for some of the machines. Depending on the computer you are interested in, savings may be minimal and you're giving up the original packaging that can also help with reselling quite a bit if you keep everything perfect.
If you use coupons at some other retailers, you can often BEAT the refurbished price for a brand new machine.
The good points of refurbished directly from Apple, sometimes they send a machine better than what you ordered, not likely, but a nice gesture, and secondly, if you are dissatisfied, Apple should be good about taking it back, and letting you buy a new one instead.