Merchant Guilds are a type of organization that are based in Klugetown. They work similar to company's in that they ware groups based around specific industries of trade or service for monetary profit. The guilds seem to lack morals and ideals aside from the search for profit.
Alliance of Trust
The Alliance of Trust is a guild. It's said that their name sounds friendlier than they truly are, but they uphold their word of trust in attempts to garner a customer base. They are likely located somewhere within "The Chimney", as with other guilds.
Artificers of Mechlement
The Artificers of Mechlement are is a guild located in Grumm's Bazaar. They're a small group of machinist who repair various goods and tools brought their way, but do not perform their goods for cheap.
The Bellwether League is an organization and Merchant Guild founded in the Airport Docks sector of Klugetown with the goal to uphold some degree of peace within the place. They were founded by captains and traders of airships, and thus have a degree of skill within the craft.
Council of Coin
The Council of Coin is an organization and Merchant Guild established in Klugetown with the express goal to create and regulate a form of legal money, rather than the trading of Jewels, Bits and Frags.
Guild of the Founders
The Guild of the Founders is a guild located in "The Rivet", an old and decreit old building. The guild was founded by none other than "The Founders", a group of very old and no-longer successful merchants.
Guild of the Helm
The Guild of the Helm is a Merchant Guild founded in Equestria founded by captains, sailors and explorers. They appear to be generally benign, mostly selling information about their adventures and pirate activity in the area. They also serve as cartographers.
The Longclaw Clan is a clan and Merchant Guild founded in Klugetown, a city in The Mysterious South. As one of the most notorious gangs in the city, they mostly operate in the Hanging Shanties, a location beneath the Airport Docks.
The Mavens are "the closest thing" to a police force in Klugetown. However, unlike other police departments, they're a business first and fight to ensure profit above all else. Typically, they act more as hired-protection than protectors of the innocent.
The Middle Monster
The Middle Monster is a Merchant Clan located in Klugetown that acts as a group of professional mediators. As their name implies, they act as a middle man organization who ensure quick deals in subtlety, "most of the time".
The Redwatch Order is a merchant guild found in Klugetown, a city in The Mysterious South. Unique to them, they are a group of magic users who collect magic artifacts in their manor in the Upper Chimney location. They have their own type of magic called "Red Magic", which is the combination of various magic types.
Smokestacks Shippers Front (SSF) is a Merchant Guild organization founded in Klugetown, however few of its members actually live there and instead travel from to and from in order to do business; a right they're very protective of. The place is located in the Chimneytop Marketplace, a locale near the infamous Airport Docks.
The Steamworks is a Merchant Guild focused around industry, with forges and factories under their control. Their major outputs are metalworks and crafts made of metal.
Thirstquenchers, Inc is a chain of hotels and taverns in Klugetown, and among its most famous businesses. They're also considered one of its many Merchant Guilds. In spite of their popularity, their quality of food and drink is apparently quite low.
Behind the scenes
Merchant Guilds are factions featured in the series My Little Pony: Tails of Equestria, in the book "Tails of Equestria: The Official Movie Sourcebook" in the article "Klugetown" in a section regarding other Merchant Guilds and factions. They were created by River Horse writer, Zak Barouh.