House of M/YMMV

Non Sequitur Episode: The nature of the crossover caused a few for some titles that tied in to it. Many Marvel comics did an issue set in the House of M reality that had little or nothing to do with those books' ongoing storylines.
Memetic Mutation: "No more mutants."
Straw Man Has a Point: Nobody actually answered Spider-Woman why it was necessary to set the world back, although the whole "humans are a persecuted minority" thing would presumably be enough to convince the heroes to change it back.
- Wanda was still a serious danger and the fact that she was so powerful she could change the history of the planet only made it clear she was even more dangerous than they imagined, since she is still mentally unstable. It's hinted that she is driving them to overthrow her after all, if subconsciously, so the fact that she's working to destroy her own world probably isn't a very good omen. Once the house of cards crashes down its also clear she didn't even like the new world, so its not hard to imagine she might have rewrote reality all over again, and again and again, until the universe is in serious peril. Granted, though, someone really should have pointed that out in-story.
Tear Jerker: When Spider-Man learns that setting the universe right would mean losing both the resurrected Gwen Stacy and the young son they had together forever. And don't get started on Uncle Ben.
- Before that, the two page spread of the notable events of Peter's life coming back to him, including the deaths of Uncle Ben & Gwen Stacy. Going through all that again, in mere seconds, and with Uncle Ben & Gwen asking if he's alright as he regains his composure? Peter immediately takes off. The other heroes all have looks on their faces that suggests that they're thinking that restoring Peter's memories wasn't the best decision, but Luke Cage sums it up perfectly.

"That was damn awful."

The Woobie: Spider-Man, after his memories are restored and he realises that Uncle Ben & Gwen Stacy should be dead. It's even noted with Shadowcat noticing that Spidey's not making his usual sarcastic remarks, and is just silently hunched over in the corner. And then in the epilogue, he desperately pleads with Doctor Strange to erase his memories of the resurrected Uncle Ben & Gwen Stacy, and his young son Richard. By the end of it, you just want someone to give the poor guy a hug.
- For that matter, Doctor Strange emerges from the event looking and sounding somewhat shattered and saying his failure as Sorcerer Supreme is to blame for it all.
Woobie, Destroyer of Worlds: Oh, Wanda...