I bought some Sea-To-Summit stuffsacks once, and found that the plastic sleeve/sheath that the bags came packed in makes the perfect stake carrier. It is more durable and puncture resistant than a fabric bag, weighs very little, and recycles something that would otherwise have been trash.
It slips easily just about anywhere in my pack (or dry bags) and I don't worry about the stakes puncturing anything. I've been using the same one for about 2 years.
Pic is of a large one, but the ones from 4L or 8L bags work great.