Besides sharing the same basic premise, Conversion Bureau stories are largely inconsistent in their continuities. Listed bellow are some of the most popular shared universes within the larger Conversion Bereau setting.
First Contact / Lost in the Herd / Midnight’s Tail Edit
This should be counted as the current manestream Conversion Bureau universe, as it is the most well-defined and most written-in definitively shared setting.
The bubble-universe of Equestria is an entirely different reality, with magical energy seeping into the human world. It is eventually fatal to humans, like radiation (a trait somewhat shared with the Yellowstone the Series set). The shield is expanding, it is ‘eating’ the planet and it is presumed that one day, it will cover everything.
The only escape is moving, and waiting, or becoming a pony.
Highlights of this universe are a genuinely darker backstory, with pollution, crime and corruption running rampant across a world almost devoid of hope for the 99% whilst the 1% live in the lap of luxury. Equestria, on the other hoof, really is everything that has been promised - bar not-perfect ponies, wild beasts and unpredictable magic. Realism (character and event-wise, these ARE pastel talking magical ponies, after all) is valued.
Stories nominally in this universe: Midnight’s Tails (tail, twist, gypsy, day the sky changed, etc), A Dinner Date, A Mare’s Tail, why, Lockdown, Change of Life, First Contact, everything by Chatoyance (see fimfiction!), An Azure Future.
This is the “new manestream”
Last Man Standing / Yellowstone Edit
This is separated here as it has one big difference, that of intent and result, otherwise it should be considered part of the “new manestream”.
Unknown to the general populous, the Conversion Bureaus are in fact the salvation for Humanity. Celestia wishes to purify the world through the use of an immensely powerful spell, and the only safe haven from the blast is in the shielded nation of Equestria. However, no human can survive the magical energies that exist there unless they undergo ponification.
Most if not all aspects of LMS have come from or have been a part of the “mainstream” universe for a long while, so this along with Yellowstone could be seen as one of the seminal Conversion Bureau AlternateAltermate Universe fics.
The prime difference between this and the expanded “original universe” setting are that the shield itself and it’s expansion is specifically engineered by Celestia, and that the resultant realm is the planet Earth, plus all that Equestria used to be.
If your Equestria will be on Earth (claimed by Equestria) then you’re in the LMS/Yellowstone universe. If your Equestria is less a planet and more a magical realm, then you may be in the “Lost in the Herd” universe. Otherwise, it’s business as usual.
Stories nominally in this universe: Last Man Standing, Yellowstone
The Conversion Bureau Edit
Blaze’s original universe. Nothing can get through the shield but ponies, and humans can’t take the magic in that pocket-universe. It may or may not be physically expanding. Humans become ponies, and many are taking the plunge.
Since the original is now one of the smallest and least-defined settings, it’s almost fair to say that IT is a fanfiction of the latter entries, and would almost certainly need to be rewritten to take a lot of the expanded mythos into account.
Stories nominally in this universe: The Conversion Bureau, Pride
Ten Rounds Edit
Further into the future, the ponies have gone from passive to active - this was a kind of subversion of the original, where niceness is actually a weapon. Ponies are more or less enslaved by Equestria and Celestia, but they like it so much and just want to help...
Stories nominally in this universe: Ten Rounds, The End, Ten Charges
Humanity, in becoming Pony, loses many of their negative emotions - but these emotions roam free and begin to take on a life of their own. Marked changes in this universe is that humans can become magical.
Stories nominally in this universe: Fragments of Regret, Last Man Standing: Aftermath
The Spectrumverse Edit
The Spectrumverse is an extensive deconstruction of the "Manestream" TCB universes, most especially the works of Chatoyance (whom the authors have professed a particularly deep dislike for). It's also possibly one of, if not the grimmest TCB fanfic universes.
Equestria's ponification plans are an explicit attack on humanity, with the barrier destroying every human and human-made object it touches. Ponification is also stated to be a "half-existence", wiping away all negative emotions and leaving the convert a perpetually smiling mockery of a pony that several characters liken to zombies. As there are two Equestrias in this story, the good Equestria is seen frequently mocking the idea of the conversion bureaus and of the usual TCB premise.
Despite its grim setting however, there is also a sense of grandiosity to the series, and the Spectrumverse is especially notable for its large cast of characters, highly detailed world building, and use of "lower deck episodes".
Stories in this universe: The Conversion Bureau: The Other Side of the Spectrum and its assorted canon side stories, as well as various alternative universe stories - notably Convergence, a crossover with The Avatar of Albion.
The Negotiationsverse Edit
The Negotioationsverse is another deconstruction of the "Manestream" TCB universe, albeit with an approach that can be described as more grounded than Spectrum's.
The series takes place on Earth after humanity (with aid from Equestrian defectors) united as one and triumphed over Equestria after a bloody conflict to stop their conversion crusade, and Twilight Sparkle, the only remaining alicorn princess, must (as the title states) negotiate a truce with humanity to save ponykind.
Stories in this universe: Negotiations and its sequels. Author RatedPonyStar gave the thumbs up for fans to write side stories in the universe.