Creator Backlash: Dave Sim himself has come to dislike some aspects of this comic. In particular he regrets how he portrayed feminism and the female characters in general, feeling they were overly idealized/simplified and unrealistic. His contributor Gerhard hated working on the thing in general as he slowly lost any ability to read it and was overworked to exhaustion. He motivated himself to work on The Last Day by repeatedly reminding himself that he would finally be done with the comic.
Creator Breakdown: And then some. In particular, it's difficult not to see a correlation between Sim's ranting about women being "leeches" and the collapse of his marriage and his resulting emotional wreck Reclusive Artist tendencies. (His ex-wife Deni Loubert was interviewed later in The Comics Journal, saying that Sim was "very scared" judging by the essay in #186.)
Fan Nickname: Fans tend to call the trade paperbacks "phonebooks" due to their size.
Flip-Flop of God: The philosophy and symbolism of the story is retconned whenever Sim's own personal views change.
The Other Darrin: Cerebus Live! where people read/performed scenes from the comic at various conventions. In the first series of skits (available here), Sim played all the roles. By the time Cerebus Live II and Cerebus Live III came around, almost all the parts had been recast and the only character Sim still played was Lord Julius.
Shrug of God: Whether Cerebus went to Hell (as the ending heavily implies) or whether he actually went to Heaven and was just panicking needlessly at the last second, as Sim hints might have actually been the case in the author's notes in the phonebook of The Last Day.