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.
Black Noir, the clone of Homelander, gleefully Eats Babies, commits murder-rapes, and eats hearts with a Slasher Smile. The villainy of the other two contenders for worst monster in the comic, Homelander and Butcher himself, was ultimately Black Noir's fault too. Black Noir drove Homelander insane by gaslighting him with the aforementioned atrocities so he would receive the sanction to kill him, which Noir thought was the only thing that gave his life meaning since he was created to kill Homelander. One of Black Noir's crimes was raping Butcher's wife Becky, which triggered Butcher's vendetta against superhumans.
John Godolkin, a twisted Expy of Professor Charles Xavier, runs his own special, private academy for "special" children. However, unlike Professor X, Godolkin simply kidnaps the children and convinces them they're special, never allowing them to go home again. The children are injected with a formula to give them powers and fill out Godolkin's many teams. However, between the ages of 6 and 9, Godolkin begins molesting the children and has the older children join in. Any who prove too troublesome are simply eliminated. Even in the dark world of The Boys, Godolkin stands out as utterly twisted.
And how did Butcher train his dog to bone on command?
Love It or Hate It: You either enjoy the book for taking apart many myths of superhero genre and corporate policies behind them or you think it's an Author Tract from guy who hates superheroes and is trying too hard to be edgy.
Moral Event Horizon: Homelander settled himself in the Believe arc, issue 46, The Muller family had just won the BELIEVE meeting prizes, a new shining car and a dinner with Homelander, the hero was kind enough to take the car and family flying to their reserved tables; that was what the family thought, the "Superhero" took the Mullers for their final ride as he dropped the car, already above the clouds with the family screaming in fear, in cold blood while revealing that the BELIEVE meeting was just a farce.
Then there was that time with him eating babies and hearts, laughing no less...
As of issue 65, the above was a subversion. That was Black Noir.
Wangst: Played with; many's the time that Wee Hughie's basically been told to shut the fuck up, stop moaning about things and just get over it by the other characters, and he does display a tendency to mope about and wallow in self-pity over the problems in his life. Then again, a lot of the people who are telling him this are themselves homicidal borderline-sociopaths who find it unsettlingly easy to shrug off various atrocities, so they probably aren't the best examples to follow in terms of getting in touch with your emotions.