Jacob's Ladder (1990)
http://www.youtube.com/watch?v=rJztRnDxdM8

Dead End (2003) - great atmospheric movie
http://www.youtube.com/watch?v=WOKRauvfkUU

The Mist (2007)
http://www.youtube.com/watch?v=E-NF55EZ5tw

Of course , there's also the famous ones like
Poltergeist
http://www.youtube.com/watch?v=5ytjaMfoF2M

The Fog
http://www.youtube.com/watch?v=nOZwnivtLbc

Alien
http://www.youtube.com/watch?v=LjLamj-b0I8

Then there's also the foreign horror movies like

R-Point
https://www.youtube.com/watch?v=Jcrj0_1F5dg

A tale of 2 sisters
https://www.youtube.com/watch?v=Hrq1JOiK6Fo

Although not usually mentioned as being an atmospheric film, I think it is a great example of perfectly executed atmosphere. The stark atmosphere that is created by the sparse use of dialogue and score along with slow pacing and stationary camera work is what makes the finale of this movie so effective.

CITY OF THE DEAD/HORROR HOTEL (1960)

^^^ Nice.  And good call on the Armando Osorio flicks.  They may not be the greatest horror movies out there but they're definitely drenched with atmosphere.

No, they're not, as I believe Return re-uses footage from Tombs and Galleon features a couple of irritating lead characters, BUT they are definitely the kind of films where you absolutely root for the ghouls to have their ghoulish way with the cast.

1. Suspiria - Not only does Goblin's nerve-jangling score keep you on edge, Argento's signature lighting and purposeful design of the dance academy give it the feel of a satanic fairytale.

2. Night of the Living Dead - Romero picked just the right creaky old stock music to accompany his groundbreaking zombie epic's starkly frightening black and white photography.  This film permeates the room with an overwhelming sense of doom and fear every time I watch it.

3. City of the Living Dead/The Beyond/House by the Cemetery:  Fulci's loosely related unholy trilogy of Lovecraftian zombie horror are perfect examples of how important sound design is in making the viewer uneasy, as each of these films practically groan with howling wind and the putridly GROSS sounds of rending flesh.  You can practically SMELL the blood and reek of decay wafting from your TV screen.  Additionally, his non-linear narratives add to the dizzying, nightmarish effects these films seem to have.  It's too bad his later films seem to have lost all these traits.

4. The Blind Dead Series (Tombs of the Blind Dead, Return of the Evil Dead, Ghost Galleon, Night of the Seagulls):  de Ossorio's Blind Dead films benefit from that oppressive, demonic chanting and the unforgettable image of his blind Templar vampire-zombies SLLLOOOOWWWWLLLY climbing from their tombs, galloping ghost-like through towns, down beaches, and across fields, then shuffling to find their victims by sound all in simple slow motion.  Though the films vary in quality (the 1st & 4th being my favorites), just the way the Templars are filmed going about their business make each film worth watching just to soak up the spectral atmosphere.

Deep Red
Black Sabbath
The House that Screamed
The Entity
The Sentinel
The Fog (1980)
The Pit and the Pendulum (1961)

I've added quite a bit to my watch list thanks to all of you.

In The Mouth of Madness
The Premature Burial
Messiah of Evil
Tomb Of Ligeia
Kill Baby Kill
Fragile
30 days of Night
The Asphyx
Who Could Kill A Child?
The Body Snatcher (1945)