These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: Darkseid. At least Mandrakk has the excuse of being a vampire and thus a victim of The Corruption; he chose Darkseid specifically because he was the worst and most dangerous thing in the universe and one most likely to bring about the destruction of reality. When he gets round to doing just that it's only because he's dying and it's little more than a giant "FUCK YOU" to the heroes and the rest of Creation for stopping him, a mixture of If I Can't Have You and Taking You with Me on an omniversal scale. This is after he begun erasing The Evils of Free Will and nearly pulling a Grand Theft Me on the entire human race with the help of the Anti-Life Equation (so his billions of victims were in a state of soul-crushing misery to boot too).
Moral Event Horizon: Inertia crossed it (again) when he killed Weather Wizard's baby son. Also Libra and Human Flame, for killing Martian Manhunter. Darkseid obviously crossed it long, long ago, but what he does in this story is certainly up there with the worst stuff he ever did.
Nightmare Fuel: The new nature of Darkseid, not to mention Mandrakk. Darkseid has transcended his physical form and become a nightmarish Eldritch Abomination who's pulling reality down into the abyss, and Mandrakk is an interdimensional vampire feeding on the death of reality. Who's heavily implied to be the original Monitor.
The release of the Anti-Life Equation, which is released on EVERY form of electronic device: TV, Internet, radio, PDA, Cellphone, GPS, etc. The book proclaims that over a billion people are enslaved this way with the initial release of the Anti-Life Equation, effectively giving Darkseid control over Earth and forcing the unaffected heroes of Earth into hiding for the second half of the storyline.
New Media Are Evil: La Résistance publishes special editions of the Daily Planet to communicate. For some reason, Darkseid doesn't bother to have the Anti-Life Equation put on posters or anything while he has Justifier slaves burning books...
At that point, he already has over 3 billion people under his control, not counting all the meta humans and others I believe. Or the mortioccus virus. Basically, at that point, he may just not care since they can't stop him.
So Cool It's Awesome: The final battle, in which Superman, Nix Uotan, the Green Lantern Corps., the Zoo Crew, the Super Young Team, the armies of Heaven itself, an army of alternate Supermen, and more team up to take down Mandrakk.
Vindicated by History: When the series was originally released, it was incredibly hard to follow, due to the series' "channel flipping" method of storytelling, the Schedule Slip that affected the essential tie-in Superman Beyond 3D, and significant Executive Meddling, particularly in regards to Countdown to Final Crisis. Now that the series has been collected properly and the readership has had time to properly digest it's contents, it's much more well regarded, with a number of readers considering it a modern classic. It's still something of a Base Breaker, though.
What an Idiot: At the end of Legion of Three Worlds, Superboy-Prime manages to break reality (again) and doom himself to being an unpowered kid in a world where everyone hates and fears him by punching out the Time Trapper who is his own future self.
Brainiac: What an idiot.
The Woobie: Overman, an alternate version of Superman who landed in the Sudetenland in 1939. He describes his world as one "built on human suffering", and it's made pretty plain he's not remotely proud of that fact. The only reason he's involved in the crisis is to find his world's version of Supergirl. And he does, but only after she's dead.