Get the Gamecube remake and you will be stunned by the even better atmosphere in that game.

I'm in doubt between Fallout 1 or Deus Ex

Lots of good suggestions here, but I nominate Cryostasis. If you can get past the horrible technical performance the atmosphere is second to none.

Agreed. Some of those last sequences, especially when you get close to Pripyat/Chernobyl, are mind-blowingly harrowing and scary.

CoP was designed with blowouts in mind though. Some of the most popular mods for SoC make massive gameplay changes that unbalance the hell out of the game. So generally I just stuck with Complete and a weapon balancing mod that made things more lethal all round.

But mods like Complete (which includes atmosfear) for CoP are mostly aesthetic, with gameplay adjusting things being optional. This makes for a much better playing experience as you know everything's been taken into account and it's not just a case of a lot of features being re-enabled which were taken out for a reason.

Don't get me wrong, I've got a lot of love for the first game, but CoP pretty much eclipses it right out of the box with modding being purely an optional extra which just adds a bit more sheen.

Yep, and don't forget the underground labs.

There are a lot of crazy mods for SoC that do unbalance the game, but I don't think that AMK is one of them. I mean, it makes the game a bit harder in general, but everything it adds feels natural and not excessive (well, maybe the artifact cooking is a bit unnecessary).

Maybe you're right about CoP having an edge out of the box though, but I still prefer SoC in general.

Games:
Stalker : shadow of chernobyl

Metro 2033

Silent hill 2

Call of Cthulhu: Dark Corners of the Earth (i forgot this too)

The Last Express

Amnesia/penumbra

Dark souls/demon souls

MOD:

The Worry of Newport

Few that pop to mind quickly:

Fallout 1/2, Amnesia, Deus ex 1 & HR, System Shock 1 & 2, Clive Barker's Undying, Call of Cthulhu Dark corners of Earth, Outcast, Mafia 1, Blade Runner, Jade Empire, UFO 1 (!), Ultima Underworld's.
Maybe even the first American Mcgee's Alice.

I also liked Dear Esther, although some hate it with passion.

--

I suppose Penumbra's and The Void would rank here as well, I just havent had the time to play them. Ive bought Anna as well, but no idea what to expect from it.

for me atmosphere is heavily supported by music...

and from what I think of right now it would have to be:

Soulbringer
first Diablo
Daemonica

in all these, when I started playing I was really there...

I agree with the people who mentioned Deus Ex and F.E.A.R. Those are some of the best, IMO.

I'm surprised nobody had said Bioshock. Like it or hate it, it was very atmospheric.

A bit of a different one here - Anomaly: Warzone Earth.

But for the absolute best, definitely the S.T.A.L.K.E.R. games.
However, I just started Metro, and it is pretty good. This could be the one that takes over.

S.T.A.L.K.E.R. absolutely tops my list with leaps advantage, other games worth mentioning are:

Hitman 1 to 4
Tomb Raider 1 to 3 (played only 1st three games so far)
Unreal
Syndicate
System Shock 1 + 2
Bioforge
Severance: Blade of Darkness
Deus Ex
Homeworld
Omikron: The Nomad Soul
Gabriel Knight series

Edit:

How could I forget Call of Cthulhu: Dark Corners of the Earth, very atmospheric this one. :)

The two games that immediately materialized before my inner eye while reading this topic were Elvira: Mistress of the Dark on my Amiga back in 1990 and Silent Hill in 1999.

Both games really scared me through their atmosphere. Of course there are those games more relying on shocking and surprising you like the Resident Evil series, but I prefer the atmospheric scares :)

Unfortunately such games have gotten more rare and I've got a hard time naming more recent candidates. Probably FEAR and Amnesia.

I mentioned these before on this thread but I think they deserve a retread as they are very indy and a lot of people have never heard of them,

The Punumbra Collection

It actually has a long list of instructions in the beginning on how to set the lighting, both in the game world and wherever you are actually playing. So long as you follow those instructions the creep factor is a can't miss. That and it has a cool combat system where you use the mouse like your arm, swinging it at baddies, opening grates, moving boxes, etc. It is kind of buggy but their are patches. And no I don't work for the makers of it, and this is not a paid endorsement.

It's a pretty atmospheric game, as were a lot of other SNES games. Don't count 'em out.

Loom