1 Rats store
In an alley, there is a large pack of rats. Stories said that if you give them gold, they will bring you interesting items in exchange. They seem highly intelligent, and will also take shiny items, food and booze. It's hard to ask them for any specific item, without a druid or ranger that can communicate properly, but not impossible.
Nobody knows where they get the things they sell.
2 The treant
You enter the store, it's a mess: some shelves are broken, their content crashed on the ground, the floor is covered in leaves and branches. Behind the counter, an enormous tree. It's too tall for the room, so its upper part is bent in a really odd way against the ceiling, covering the entire room with its branches.
You notice there is a face in the wood, a mouth opens, and with a deep voice that makes the whole building shake, it speaks "Welcome, how can I.... uh... help you lil' saplings... ye?"
This treant always liked humans, for some reason, and dreamed of experiencing their life. One day, he stopped some wolves attacking a merchant that was going through the forest, in exchange the merchant hired the treant in his shop.
He's pretty terrible: goofy, slow and destructive, often breaking things when he moves his branches around, but he's trying and slowly improving.
3 the alley
There is a back alley in the shadiest part of town, in it, you'll find an even smaller alley, barely large enough for one person, nestled between tall houses. It's dark and damp, hard to breath.
Go there at midnight, place a bag full of god at the very end of the alley, with a note saying what you item you need. Then, take a knife, cut yourself and drop some blood on the street stones.
At midday the next day, if the gold was enough, you will find what you wanted in the same place. If it wasn't, you'll find a severed pig head, with a similar but not-quite-the-same item in its mouth.
4 The cleric of the god of lies
Apparently a normal shop with a very friendly and generous owner, this place is built above a temple to the trickster god, and the shopkeeper its cleric.
Every item sold here has a drawback: potions are mislabelled, many items are cursed, armours have holes or missing parts. Their rope is too short, their lanterns give out bright pink light, their thieves tools always break, their backpack is always wet and ruins what's in it. Their blankets make you itch etc.
They do it just to fuck with people, for fun. If caught, they will say they have been cursed and send the players on a fool's errand to remove it, while they run away.
5 The barbarian
This store is owned by a violent barbarian that wants gold to buy food and booze. He has no concept of personal space and is very touchy, if a client asks for a "lame" item he'll laugh and offer something else, if the client looks like a nerd (mage) he'll make fun of them.
He likes bartering, but has no interest in items that seem weak or unworthy of a warrior, and will handle them very roughly. Don't sell anything made of glass to him, he'll just throw it at you laughing.
6 The pit
In the middle of town is a strange pit, throw something in it and a pale, long tentacle will emerge from the darkness, giving you something of equal value in exchange, sometimes.
Some have tried going inside, they all came back but couldn't remember what was there.
7 The bog
There is an isolated bog, not too far from town. Make the correct signal at night and from the tar a whole shop will emerge. It's a black market store, with many rare and illegal items, that magically hides inside the bog for safety. The people working in it are all slender humanoid frogs with a lucid black skin.
8 The paranoid
There is a store hidden by a 3 meters tall wall, it has no visible windows, only a steel door. Inside, you'll find yourself in a completely empty room with only a chair and another metal door with a hole in it.
The owner is extremely paranoic and mysterious. Only one person can go in the store at once, has to sit on the chair and ask what they want. The shopkeeper will talk to them from behind the door, and procure the item they want.
The gold must be put on a tray that goes under the door, and the item will be dropped from the slit in the door.
The buyer never sees the owner, any attempt to enter or spy on them with magic will find it's extremely hard. The room with the chair can be flooded with toxic gas if clients aren't following the rules.
The owner is always there, always the same person, but if you listen very well, you may notice he's often whispering to someone else behind the door, and there are multiple voices.
9 The space-shifted
This store exists in a dozen locations at once. The same shopkeeper has the same inventory and works in all the stores at the same time. Clients will see strange, evanescent figures moving around: those are reflections of people in the other stores. They will see a haze around the owner, he will look blurry and stretched.
That's because he's dealing with someone else somewhere else.
The store can be used to move things to distant places rapidly (give a coin to the owner, he can give it instantly to any person in any of the other stores), but not living creatures.
The players enter the store and behind the counter is... the players.
They will be very friendly with themselves, but refuse to answer any question: all they can say is that time-travel is involved, they'll see in the future, it's fine, no need to worry.
Saying anything could cause a paradox, so they can't, but they can still sell them things. And they already know what they will buy, because they already bought them in their past, the players present.
bonus points if you can imitate your player's voices.
Edit - some great suggestions for more shops in the comments
The involuntary shopkeeper / The prancing kobold / Gran's house / The teleporting shack / The dragon shop keeper / The sacrificial stone / The strange crate / Okail and Halite's Enchantments / A warlock multi-level marketing scheme / the shop that sells itself / Gaiman Nancy's Always Open book shop and supplies / The Alchemist