I take them all out of the box. If there is a cool picture in the background I will try to carefully open it and keep the back cardboard, but usually I just get rid of the box.
Speaking of ruining collectible value, I also paint some of them for fun. I am currently turning Epona Link into Ezio from Assassin's Creed and I want to make male Corrin into Lord Ghirahim.
All mine are out of the box. The packaging gets binned. I'm not a serious collector, I just like having them on my shelf.