A list of working combos found so far:
Positive:
[Group A] : Blacksmith, Armory, Weaponry.
[Group B] : Witchcraft, Potion Shop, Gem Shop, Fortune Teller.
[Group C] : Barbershop, Wardrobe, Jewelry.
[Group D] : Pottery, Furniture, Wagon.
[Group E] : Brewery, Tavern, BBQ, Eatery.
[Group F] : Book Store, Medicine, Terrace.
[Group G] : Live Stock, Soup, Fruit Stall, Butcher.
[Group H] : Colosseum, Bestiary, Bowling.
[Group I.1] : Trading Post with Snack and Music Hall.
[Group I.2] : Trading Post with all General Stores and all Food Centers.
[Group J] : Restroom, Elevator.
Neutral/Negative:
[Restroom] : Neutral to almost everything but negative with BBQ, Brewery, Eatery, Tavern
and positive with Elevator
[Snack] : Neutral to everything but positive with the Trading Post.
Certain store and food combinations are negative.
Here's link to a comprehensive compatibility list for Shop Empire 2:
http://shopempire2.wikia.com/wiki/Building_Compatibilities
Most useful for optimizing the layout.