A general list of groups and organisations characters may be loyal to!
Shopkeepers
For every secret underworld of magic users, there are those who can supply them with what they need. The Shopkeepers (not shopkeepers) are a global cabal of neutrally aligned keepers of magical stores and travelling merchants. They buy and sell magical ingredients, sometimes information, but take no sides in a conflict and maintain a policy of keeping to themselves and what benefits their business. That being said, their personal morals away from business vary wildly; they can be as malevolent or as benevolent as magic users are in general. Most Shopkeepers are human, and those who aren't generally appear human. The easiest way to do business is to disguise it in plain sight after all, and Shopkeepers often have a secondary business (antiques, fortune telling, model railway supplies, etc.) that they sell to regular humans. Shopkeepers are often magic users to some degree, at least enough to be able to identify and work with the things they sell. Crossing or harming a Shopkeeper significantly while in the course of business runs the risk of putting you on a worldwide blacklist, their services forever unavailable to you no matter where you might inquire.
The Vampire Queen
According to the tyrant queen and her forces, all vampires are currently under her rule unless they forcibly resist it, but in practice every vampire may have a differing opinion or level of loyalty. Those who are truly loyal to the queen in name though may have a special position, or report to some of her own organisational forces:
Hazards: - The vampires with the queen's authority to act in her name and the authority to kill other vampires if necessary are known as the Hazards. Generally there are 1 or 2 per major city, and they are usually dangerous older vampires. They function as a sort of sheriff for the area, with other lower vampires ("snitches") reporting to them. Hazards are usually somewhat known in their area but can otherwise be identified by the rings they wear with a black stone.
Whiteeyes: - One of the queen's Hazards, known as the Duke, is the sire of the Whiteeye vampire bloodline. Whiteeyes are a widespread family network of vampires that specialise in blending among the homeless, and their excellent spying abilities as a result mean that the information they gather may reach the ears of the queen via the Duke. Whiteeyes are essentially the tyrant queen's spy and intelligence network.
The Institute - (created by trilonibble)
The Institute of Teratological Regulation is an organization of monster hunters and researchers dedicated to culling dangerous supernatural entities. Its main directive is to protect humanity from the predators that assail it from the shadows, though its politices have mellowed since its 19th century founding from total eradication to merely eliminating the cruelest and most ravenous. The Institute maintains a network of hunters specialized for certain quarry, such as vampires or witches or merfolk, and its archives contain more than a century's worth of data gathered about magical creatures from around the globe. While the Institute's main facility is based in Scotland, it has no official affiliation with any government, and most of its agents are mobilized across the world to investigate potential targets.
Shadowy Government Organisations™
What are they up to? Nobody knows. Seems a given however, that there are some divisions in the upper echelons of various major governments that have knowledge of the supernatural and may possibly working against it. Or perhaps want to use it for themselves? Kept deliberately vague and hush-hush, if you want to create your own branch of this or leave it ~mysterious~ that is entirely up to you.
The Yes You Can Carnival
Although barely qualifiable as a faction, the Yes You Can Carnival is a travelling carnival founded and managed by the vampire known as Carnie that welcomes the scraps and oddities of the supernatural. Creatures who struggle to wear the mask that the modern supernatural world must hide behind, oddities like werewolves who hate being in a pack, or humans irreparably affected by magic or other supernatural forces... many of those who fit nowhere else can be found here. The carnival keeps to itself, focusing on taking care of its members and putting on a spectacular show for its human patrons. Like all carnie folk however, its members are generally very suspicious of all outsiders and only loyal to each other, and perhaps not completely to be trusted if you aren't part of their extended family.