So after Heather kills the god, she mourns, then gets up to leave. Before she exits the room, she sees something behind her that makes her gasp. The Book of Lost Memories addresses this moment... by literally asking the very same question I'm asking. It doesn't have any insight on the matter at all; it just says "what was it that she saw?"
Since the game gave us so little to go on, all I can do is guess. Maybe Valtiel's pissed and is attacking her. Maybe Alessa's ghost is showing up to pat her on the back. Maybe the dying god twitched. Maybe it was Ashton Kutcher, telling her she's been Punk'd.
While the Ashton Kutcher one definitely seems the most plausible do we not hear the faint sounds of a baby crying right before Heather turns around? It's been years since I played so my memory's fuzzy on this. If it is the sounds of a baby, I always thought of it symbolizing that God has been reborn, yet again, continuing the legacy of what makes Silent Hill.
Possibly... I just watched the clip again on YouTube and I think I might hear a baby sound, but it sort of blends into the music, so it's hard to tell. (I wouldn't have noticed this when I actually played because I had the volume fairly low to avoid waking a friend's parents.)
But now that I watch it again, it doesn't really look like she's even gasping or shocked by what she sees. I think the note about it in the Book of Lost Memories over-hyped it in my memory or something... I'm starting to think there's nothing to analyze here and that maybe she was just looking back at the dead god.
certainly seems the most plausible, we do not hear the faint sound of a baby crying just before Heather turns around? It's been years since I played so my memory is fuzzy on this. If this is the sound of a baby.
Although my post doesn't support anything new as option, I surely go with the apparition of Harry. I am pretty sure that, for the first time after seeing her father on his death chair, Heather felt the need to break down because she couldn't hold on strong anymore. How could she, after all these fights, let alone the final fight with god. When your defenses are down, the sadness and nostalgia for a long lost beloved person is the first thing that comes to your head, so you really break at that time. Apart from that, it is poetical to think Heather saw Harry, because it's like a backwards scene from the one we experienced in the original Silent Hill: Harry kills Samael, then he sees his daughter as redemption before he exits the nightmare. In Silent Hill 3, Heather kills god, then she sees her father before she exits her nightmare. Makes sense, it's purifying and adds to the magnificent drama.
I'm gonna go with Harry's apparition, the same theory I stuck with since I saw that scene. I don't see why she'd turn around and be surprised by the God since she clearly pwned it already, and why would she be shocked to see Douglas? She *was* surprised at something. The sound of a baby crying was removed from the final game. You guys probably heard that in the Making of Silent Hill 3.
In Nowhere, Heather can find a room which is an exact replica of Harry's room in their apartment. One glaring missing element is that Harry's corpse isn't there on the bed anymore, yet there is blood stained on the mattress (sheets gone too for some reason) and a blood trail leading to the door. There is a necklace or jewelry of some sort left behind, as well as one of his journal entries. Harry evidently either was left to wander the Otherworld forever (or perhaps until Heather/Cheryl/Alessa ended the God and Claudia).
One could think that Harry was only bound to the Otherworld due to Claudia's influence, as she is the reason why the influence of the town spread out so far beyond Silent Hill. Perhaps Heather turned around and saw her dad, which gave her some solace, as she is clearly happy right after this scene when talking to Douglas.
Never confirmed what she saw and never will be, but this makes the most sense to me.