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First, to clarify some terminology defining the different types of crossovers, which we need for mapping the Omniverse.
Type 1 - Interdimensional
The "strongest" crossovers are the ones involving interdimensional travel. Simply put, most superheroes can't live on the same world as ones published by other companies because major conflicts tend to arise over time about how the world and the greater universe is structured. Hence, stories where some of the characters are explicitly shown to travel from their own version of Earth to the world of the other heroes involved avoid that problem - they can't be ruled "non-canon" due to differences between the versions of Earth depicted in the regular comics because at least one party isn't on their native world.
Types 2 and 3 - Merging and Commonality
Sometimes crossovers happen without any explanation of how the disparate characters come to share a world. The simplest answer (and not counted as an Omniversal crossover for our mapping purposes) is that they do just share a world - if the established histories of the characters involved doesn't prevent this, then why not? Using a TV example, there's no real reason why CSI and Without a Trace can't coexist in the same world, or a bunch of Westerns can't all be taking place in the same version of Earth. However, sometimes the different backgrounds are pretty incompatible - Savage Dragon has met Hellboy a couple of times, but some of the demonic problems Hellboy's Earth has faced should have gone very differently if Hellboy's world was full of all the Image Comics superheroes to help fight the threat. This is where merging crossovers and commonality crossovers come in.
Merging is when the historically incompatible worlds of two characters temporarily combine to become a single world - imagine the realities are like bubbles floating in the cosmos, moving around and occasionally bumping into one another, briefly intertwining, and then splitting apart again. While they are intertwined, the inhabitants of the merged world don't know anything is different - memories alter to incorporate the inhabitants of both worlds seamlessly (more or less), and they think they've always shared a world. This is an established idea in the comics, though maybe not often explicitly stated. We've seen it in reverse: Image Comics began as one shared universe, but the Shattered Image miniseries depicted the merged worlds of the different founders splitting apart - and when they did, new characters appeared to fill the gaps in the world left by the people now belonging to a different world (e.g. Mr Majestic came into existence to replace Supreme), while memories altered so no one noticed the lost ones' departures and the new ones' arrivals. And we've seen merges happen - at the end of DC's Crisis On Infinite Earths, DC's multiverse merged into a single world. Years later it was established that this wasn't a new world, but the merged version of the old ones. Power Girl of Earth 2 had been the cousin of Superman of Earth 2; in the new Earth, that history was incompatible because Superman was Krypton's sole survivor, so Power Girl got a new origin (actually, a couple, as writers struggled to find one they liked); during Infinite Crisis, Power Girl learned these origins were fake, and the reason they'd kept apparently changing was because the merged Earth was trying to fit her anomalous presence in, altering memories to do so - but in truth she was and always had been the Kryptonian Earth 2 Power Girl (Infinite Crisis #2, when Lois Lane of Earth-2 touched Power Girl, restoring her memories). It should be noted that some mergers are largely seamless - everyone's memories alter to include recollections of the new inhabitants now sharing their world; others are smooth but not seamless (CoIE is an example), where most people don't have major revisions to their histories and memories, but a few do; and some are train wrecks, as characters have their histories violently altered or even become merged into combined versions of one another - this latter type seems to be dangerous to the fabric of the Omniverse, as those who protect the Omniverse rush to try and split the realities apart again ASAP. Examples of this last include the crossover events Amalgam, Worlds Collide and House of M, and, in novels, the X-Men Chaos Engine trilogy.
Commonality is weaker evidence towards the Omniverse, because strictly speaking it isn't showing any crossing over. Batman has run into Sherlock Holmes, so Sherlock Holmes exists in the DC universe. In Marvel Comics, the son of Fu Manchu is Shang-Chi, and his ally Clive Reston is Sherlock Holmes' grandson, so Sherlock Holmes exists in the Marvel universe. But the Marvel universe is demonstrably not the DC universe, Sherlock Holmes is unlikely to be dimension travelling, offspring (a lasting effect) would seem to rule out the "Sherlock Holmesverse" as simply having merged with Marvel temporarily, and Sherlock Holmes' own baseline (the Conan Doyle canon) are incompatible with Marvel's Victorian England, as the latter had superhumans in it. Commonality seems the best bet - simply put, some characters have widespread counterparts across the Omniverse (see counterparts vs analogues below); they are common to many worlds. Hellboy (to use another example) has met the Savage Dragon a number of times, but he might not be the Hellboy of Mike Mignola's Hellboy comics - instead, he could be Hellboy's counterpart in the Image universe. Commonality is still evidence of a shared Omniverse, as in theory every world that contains Spider-Man (for example) is part of the Marvel multiverse, but it's evidence, rather than the outright proof that an interdimensional crossover provides.
How can we tell which of the above we have when there's a crossover with no explanation of how the characters have come to share a world? There's no definitive way, but a good indicator is if the story is ever referenced back to. If one character mentions the encounter later, then it may well be a commonality - the other character exists in their world; if neither one mentions it, or both do, then it's likely to be a merger - most (but not all of the time) characters forget their encounter after a merger ends, so neither mentioning it supports that possibility, while both mentioning it means it "happened" for the "real" versions of both characters, not for a version of them on another world. However, for iconic characters like Sherlock Holmes, commonality is usually the best assumption.
Type 4 - Parallel Lives
A version of commonality, only this time, EVERYONE is a counterpart, not the "real version," and they all always share the same world. A good example of this would appear to be the Marvel/DC crossovers of the early 1980s, where the Marvel heroes and DC heroes clearly shared a world and knew of one another's exploits. Arguably of course, this could just be an example of a merger. How do we tell the difference? Best bet is that if all the characters have long histories but yet this is the first time they have happened to meet one another, despite supposedly sharing a world for years, then the worlds are probably merged. If they remember past encounters, then it's parallel lives. Again, parallel worlds which just happen to share inhabitants are evidence but not confirmed proof of the Omniverse - but if every world that contains Superman is part of DC's multiverse, and every world that contains Spider-Man is part of Marvel's multiverse, then a world that hosts both belongs to both multiverses, and hence proves a multiverse overlap, which is evidence of an overall shared Omniverse.
Counterparts vs. Analogues
In real world terms, when one company creates someone iconic, sooner or later other creators do their own take on the idea. In fictional terms, this means we have what are termed analogues. Counterparts are when the same (or largely the same) character can be found on other worlds - Earth 1's Superman was a counterpart to Earth 2's Superman; they had minor differences in their backgrounds, powers and appearance, but they were unquestionably the same person. Importantly for our purposes here, counterparts are considered evidence that the two realities the counterparts are native to share the same multiverse. Analogues are when events work to shape a similar, but not identical, character - Marvel's Hyperion shares a lot of similarities to Superman (last survivors of their species, similar powers, etc), but (legally at least) they aren't the same person, though they fulfill the same basic role within their worlds much of the time. At exactly what level of change someone switches from being a counterpart to an analogue isn't a clear line, but usually you can easily tell which is which. For the purpose of forging links, counterparts are considered evidence of Omniversal connections, albeit weaker than a proper crossover, but analogues aren't counted, as they don't in themselves prove that realities share a multiverse.
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