Hi
I think much of it is personal preference. I like to frame my pins, my son keeps them in pin bags, his father keeps them in a binder.
Most of my traders are in my trader bag. Some I keep in the packaging they come in if I just going to trade them anyway. The DS ones I am trading I keep in the packages just because I am too lazy to open them and put them in the bag!
I have some framed, some in the original boxes, some in the original packaging, some in binders, some in original packaging in the binders....
Depends on if the card helps make the pin, if it is an LE, if I plan to keep or trade it, etc.