During his frightening hospital gurney ride in the intro, Alex sees several terrible things happening to some of the people in nearby rooms; physicians apparently murdering patients. One's being cut to pieces, one's being strangled, and one's being buried in a pit. Much much much later, we find out this is how the missing children died.
Lots of people rolled their eyes at the fact that Pyramid Head is even IN Homecoming, claiming that he's just there for fanservice and has nothing to do with his original portrayal by this point. Until the endgame, this appears to have at least a grain of truth to it - Pyramid Head, while still scary as hell when he shows up, doesn't really do anything to Alex, outright ignoring him at one point. Then you find out who PH is REALLY after, and it all makes sense. In Silent Hill 2, Pyramid Head was, according to designer commentary, either a twisted reflection of James' guilt, or Silent Hill's method of punishment for grave sins. Both of these interpretations make total sense when you realize that PH isn't after Alex, but his father.
The latter interpretation is taken in this game, and instead of sinister paintings, this time there are child-like drawings depicting Pyramid Head as a "bogeyman" who punishes children for stepping out of line, seeing no difference in the severity of sins and putting children through awful punishments for even slight disobedience. The bullet directly above comes into play in Hell House, where a medal that was ordinary in the Fog World is re-designed to appear as Pyramid Head's helm, and placed on Adam's jacket. "Bogeymen" aren't real, they're just there for parents to enforce obedience from kids, but it makes no difference: Adam's atrocious parenting made the Bogeyman very real for Alex on a daily basis.
Which adds an extra bit of Fridge Brilliance to the "Bogeyman" ending. What seems like an odd note to end the game on becomes a bit clearer when you realize PH's true purpose as covered above. Each of the parents that were marked for punishment were discovered by Alex and promptly dispatched (with Alex himself dealing with Holloway) before Pyramid Head was able to reach them. By not forgiving his father or mercy killing his mother, he was ensuring they suffered as much as possible for their actions, as fits the general description of Pyramid Head's purpose. By taking matters into his own hands and enacting punishment, Alex made himself fit to be the latest judge, jury, and executioner of Silent Hill.
Moreover, the Bogeyman ending also meshes excellently with the Sins of Our Fathers theme the whole game has going on. Alex becomes a monster, because that's what his family and his community made him into. He is just as much a victim of their sins as the murdered children. It just took longer for him to be embraced by the darkness and strike back the way they did.
What was the point of all of the torture Margaret Holloway and her recuperated neo-Order cult were inflicting on Alex, Elle, Wheeler, and the townspeople? Why not offer the choice: join, or die, and make the point with a bullet? Particularly with Alex, whose survival is the entire centerpoint of her vicious retribution? Shouldn't she want to just kill him to appease God? But then, if you remember, God is a force that can be summoned in physical form. There's been threepreviousattempts already. The rituals for such a thing are nebulous, but can essentially be boiled down to "intense suffering on a helpless individual who will then become its host", thus Dahlia burning Alessa alive and Claudia putting a hit on Harry. Margaret was torturing Alex in an attempt to pull God into the world, so she could then kill it and end the nightmare.
As mentioned on the main Silent Hill page, the Siam enemy has so much symbolism relating to James and Mary attached to it... what if it's actually the two of them, still trapped in Silent Hill forever?
Shepherd's Glen is now a permanent offshoot of Silent Hill's haunted mess. However, the pact that results in this was made before Alessa's time. Who's really in control of Shepherd's Glen, Alessa's will or the demons?
Going on that, a majority of the game's endings are inarguably bad, but there is one good one. Except...it's still a horrible outcome for Alex. He was in a mental asylum for four years and can't prove it. Because his home is now severely and irreparably haunted, he can't prove he finished or even went to high school. Getting a job will be extremely difficult or impossible that way, and he will have to find a place to live. And that's without the borderline useless leg that Holloway left him. He's likely extremely traumatized and recovery will be difficult. His life will be as a hermit who, judging by the way things have gone, will have a horrible time staying afloat.
Even worse? This means that, really, the Bogeyman ending is the best one for Alex. Yeah, he loses his humanity and becomes a demon, but he becomes an immortal avenger who will spend the rest of his existence dealing out torturous deaths to bastards who deserve it, just like the adults of Shepherd's Glen. He becomes a monster because that is what they made of him.
The usual trappings of the Silent Hill's Order mythos usually center on God's rebirth, and thus the introduction of its "paradise" (implied to be the apocalypse). With no Alessa around to stop it, who's to say the dissolution of the Shepherd's Glen pact has not released God into the world already? How long does the world at large have before everything goes to shit?