Downtown Disney is split 3 ways, you have the Marketplace, Pleasure Island and the Westside. Most of the shops on the westside are Participant Companies that rent space from Disney to have their stores (so they are not Disney stores...for the most part). Here is a list of the Westside shops:
Cirque du Soleil boutique
DisneyQuest Emporium
Disney's Candy Cauldron
House of Blues Company Store
Hoypoloi Gallery
Magic Masters
Magnetron
Mickey's Groove
Planet Hollywood on Location
Pop Gallery
Sosa Family Cigars
Starabilias
Sunglass Icon
Virgin Megastore