Most stores have at least a small rack of pins, but LE pins are
Animal Kingdom - Island Mercantile (large store on left side, as you look at the Tree of Life)
Epcot - Pin Central (back side of the wait times board)
Hollywood Studios - I forget what it's called, Sunset Market Ranch? It's on the left side of Sunset Blvd if you are walking toward Tower of Terror
Magic Kingdom - Frontierland Trading Post (across the breezeway from Country Bear Jamboree)
Contemporary Resort - Fantasia Gifts (Toy store in the center of the 4th floor concourse)
Downtown Disney - Pin Traders (open air pavilion across from Once Upon a Toy)
Pop Century - I've found a limited selection of some LE pins, in the case in the shop.
Aside from that, the large stores like Emporium, Mickey's of Hollywood, and Mouse Gear also have many racks of open edition pins, mystery boxes, etc. There are several pin carts too: Tomorrowland, World Showcase between UK and Canada, and American Adventure, Africa on the pathway toward Asia. And any resort.