I read half of the topic and there are some people added brilliant ideas to make a scary game!
Since I haven't read everything, my apologies if I add something that was already said. I also don't know if those would be easy gameplay elements to implement.
I myself think that Amnesia could have been better, starting with the monsters: once you know the "trick" on how monsters work in the game, you can actually use the system to work things around and learn how to easily avoid the monsters. When I started playing Amnesia I did some stupid things for fun, like running after some of the monsters when they were appearing because of a scrip, and surviving an encounter that should have been the end for me normally! If you play the game as it is intended to be, then you're in for a ride of horror. However, if you fool around, you might actually end up having less trouble with the monsters!
First of all, I should point out what really worked: the sound effects, both the growls and the "scary/insanity" sound coupled with the effects on screen when a monster was getting closer: that easily made up for 50% of the terror that could come from the monsters. Their design was great also, rather terrifying while staying quite simple (which is hard to do, sometimes when you start designing weird and completely crazy monsters you take the risk that they won't be ultimately be scary) the first time I really saw one of them I had so say aloud "Oh boy! He's ugly!" while feeling a little chill on my spine.
From what I got, monsters will spawn at certain key moments (entering a new place, finding an object, solving an enigma), with the music changing. All you need as a player is to find a place to hide and wait for the "scary music" to go off, since that will mean the monsters will have despawned. Monsters are pretty stupid, and won't think about searching an area by opening many doors (though I can understand that in very small areas it would make it impossible to escape the monsters).
This brings two problems: first players can expect when a monster will appear. Secondly, players will know that as soon as the music will stop they won't have anything else to fear, because that would mean that the monster despawned.
In my opinion, those scary moments would have been more efficient if there was a percentage of change that monsters would not despawned. I would have also kept the "monster music" going on for more minutes, so players would doubt if the monster was still around the level or not.
Also, I don't recall facing directly a monster after opening a door, except one special time with a script (I actually slammed the door at the monster face, ran to hide, and realized the monster wasn't even trying to bash it down...), or suddenly in a corridor, etc. In other words, since it is easy to guess when monsters will appear, players have almost always the opportunity to prepare a "hidding spot" somewhere in the room before doing anything in it: by doing so I've saved myself many times in the game.
So on top of the scripted monsters, the level should randomly spawn a monster somewhere, pretty much like in the Aliens vs Predator game that came out 10 years ago for the PC: you could never stop and hide in darkness for too long, since there was a risk that a spawned alien will find you.
On top of that, it would make the levels way more stressful: I was somethings running around some levels with no worries, knowing perfectly that no monster was suddenly going to appear in the corridor in front of me.
Something else that bugged me was the fact that the monsters were pretty much harmless once you knew you would respawn at the beginning of the level, while the monsters will actually despawn sometimes! I remember, once in the sewers, I was pretty low on health and a monsters had just spawned nearby: I allowed him to kill me, I was back with almost full health. A little bit later, after being killed again, the monster mysteriously despawned: all of those little things made the game actually easier in my opinion. No full health back after being killed.
While I agree you can see in low light, I didn't like the fact that Daniel could see in fulldarkness!
Someone had an idea I really liked: a room with a flickering light and a monster in it...But the room is in total darkness, so you can't see anything but when the light is flickering. It would also make the monster scarier, since you would only see glimpses of it.
More monsters would have definitely been a big plus, all of that coupled with sanity: when you sanity is low, some of the monsters you see are fake, and will not harm you, but you would still think they are real (same visual effects, same music), and then you run into a real one but think it's an illusion...You guess the rest.
As for special scary moments on the game, hm, dunno. I think those were already mentioned: solving a puzzle in some limited time, otherwise a monster will get us. Leaving an area without being noticed by a very dangerous monster that is wandering in the area.
And personally, I would have loved to have a glimpse of something "big" and "huge" around the end of the game, a glimpse of some sort of "Great Old Ones"
I think I was a little bit disappointed by the end of the game: then tension went a bit down for me once I reached the Inner Sanctum.
Anyway, those are my two cents, hope they might be useful!