I threw out all my boxes, frankly because they add to the bulk and I have limited storage space.
* They keep light out, which is a good thing. Sunlight is reportedly bad for whisky.
* They protect the bottle. When you're paying premium prices, it's nice to have some protection for that investment, even if its just a thin piece of cardboard.
* Look cool. Indeed, the manufacturers spent a lot of money (that you in turn paid them) to put their bottle in a nice box. You might as well enjoy the benefits of your hard-earned cash, and leave them in the box!
Welcome, and good luck with your Glen. 12yr. To me, its too close to a blended to get me excited. However, once you enjoy the Glen. 12yr, and start to discern the various flavors, you can figure out what you like and dislike, and will have better luck finding your way around Scotland (at least its whiskies!)