So I will try to remember every bit of it. Most of this is off the top of my head.
Anyway, the point is that some people think there is nothing supernatural to SH2. There absolutely is. It's just way more covert than the original game and subsequent ones. I made a list of all the things I could think of...
Main game:
- -Occult paraphernalia in the prison cells. This includes the wax doll, books on summoning fallen angels (etc), and sigils drawn on the wall.
-The faded Seal of Metatrons [?] found when fighting the two pyramid heads.
-Monsters being manifested as James's problems. There's at least one monster that is a remnant of Alessa's nightmare; the bugs. (This one has nothing to do with James.)
-The sound of prisoners' rattling the bars in their cells and the sound of the hooves of horses near the executioner's post.
-The tome, obsidian goblet, white oil, as ritual items. (Implied to be for the red god, Xuchilpaba [AKA Xuchilbara], as a part of the Crimson Ceremony to resurrect the dead.)
-The Book of Lost Memories mentions that there are spirits everywhere. Not just of dead ancestors, but spirits of nature as well.
-"Feast of the Gods" painting in the prison that depicts Jimmy Stone performing a ceremony in front of an audience. The Valtiel Sect, of which Stone is a priest of, is tied to the indigenous religious cult of the area; The Order. (1)
-In a related part of the lore, the stone monument states that many executions were done in Silent Hill and because of the blood spilled, with the emotion, there is many ghost sightings in the area. This appears to relate to the Occult magazine memo found in SH3. (3) This is expanded on in The Book of Lost Memories. (4)
-In the otherworld time and physical limitations are transcended; thoughts of people are communicated and connected. This explains the enigmatic letters from the Brookhaven director to James in the 2nd game. For example, he seems to know things about James without even meeting him. (ibid 4)
-Maria has Mary's memories. This is further seen in Born From A Wish, where she remembers Laura despite never knowing her nor James. (Is she the reincarnation of Mary?)
-It is implied that a heater burned down the Lakeview Hotel. The heater even has a note on it that says "I'm Johnny, one hot guy.". (5) If previous lore is added up, it appears the Order may be behind this as they did not take kindly to the town being developed. It is implied in (6) that the Order cursed the developers and almost directly stated in (7) that the Order cursed many people who got in their way. (They died mysterious deaths as a result.) So, it could be that the mystery heater fire of the hotel, was a result of such shenanigans. (The Old Gods don't take kindly to the town being turned into a tourist attraction, it seems.)
-Native American like chants in the form of tunes can be heard in the laybrinth. (8)
-Maria comes back to life multiple times.
-References to sin and sinners are scattered in the game. Mostly as implication. But with the 3 tablets at the prison are specifically referring to Angela, Eddie, and James, and their sins, respectively.
- -Maria has Mary's memories.
-With the boards, they detail aspects of the religion of Silent Hill. In the white board, "spirit of the mist" is referenced and is possibly implying Xuchilpaba. The black board references "You Who Deny Death". The red board states "oh you gods deep in slumber".
- In the memo about acacia, it is mentioned as a symbol of immortality in multiple religions. Ishtar, the Babylonian goddess of fertility and war, the Queen of Heaven and Earth, is mentioned in conjunction with acacia. (This is because, Ishtar, also known as the Sumerian "Inanna", came back from the dead in one famous story.)
-In the Book of Lost Memories memo is talks about the old Native religion and how they believed in death was not an end but that they thought the deceased merely returned to nature. They also thought the process was reversible. The same memo mentions the god Xuchilpaba and their salvation, while having notes about the ritual items for the Crimson Ceremony. (Though the names are slightly variant, this "Xuchilpaba" is probably the same as the red god Xuchilbara mentioned in the paintings in SH3. Hence the "crimson" (another shade of red) being mentioned in conjunction with them.)
-On the tombstone, gods are mentioned.
-There is graffiti outside the mansion that says that the house is haunted. This turns out to be true, as Ernest is a ghost.
-Ernest figures out why Maria can hear him, when others cannot. But this reason is implied that Maria came back from the dead. He tells here the gods are there [in Silent Hill] and she can feel it too, because she was born in the town. Maria simply retorts "I'm not sure 'gods' is the right word for it.'