I don't run stores but I like stores that sell things that I might not want to go through the trouble of collecting or keeping on hand later.
Crystal/metal store. Has every type. If it's new-agey or themed it's a bonus.
Herbalism store. All things herbalism. Potions and salves. One of each insect type. A greenhouse off to the side with herbalism plants and related plants needed. Sometimes for some reason buying individual plants doesn't seem to work for me so...
Ambrosia cafe. Might have other items also... Sometimes you want to bring a ghost to life and don't want to get all that stuff together.
Science type store that might sell those potions from GTW but definitely has Xenopetrium. Plants from Sixam and crystals are a plus.