1. If characters A and B have met, then they are in the same universe; if characters B and C have met, then, transitively, A and C are in the same universe.
2. Characters cannot be connected by real people — otherwise, it could be argued that Superman and the Fantastic Four were in the same universe, as Superman met John F. Kennedy, Kennedy met Neil Armstrong, and Armstrong met the Fantastic Four.
3. Characters cannot be connected by characters "that do not originate with the publisher" — otherwise it could be argued that Superman and the Fantastic Four were in the same universe, as both met Hercules.
4. Specific fictionalized versions of real people — for instance, the version of Jerry Lewis from DC Comics' The Adventures of Jerry Lewis, who was distinct from the real Jerry Lewis in that he had a housekeeper with magical powers — can be used as connections; this also applies to specific versions of public-domain fictional characters, such as Marvel Comics' version of Hercules or DC Comics' version of Robin Hood.
5. Characters are only considered to have met if they appeared together in a story; therefore, characters who simply appeared on the same front cover are not necessarily in the same universe.