Suspiria is VERY high up there for me. It's style, it's score and it's direction are as perfect as you're likely to see within the genre.
(I know you said post 000's, but just for anyone who might be interested in general...)
Rosemarys Baby
The Thing
Evil Dead
The Shining
Raw
Alien
Re-Animator (those it's more a comedy at this point)
The Babadook
The Vanishing
Mullholland Drive
Eraserhead
Ring (both versions are good in there own ways)
The Devils Backbone
Possession
Jacobs Ladder
Meshes In The Afternoon scares the sense out of me every time
Let The Right One In
Anything by Cronenberg gives me the damn willies
There's probably a thousand more that I'm missing here. Horror is such hugely varied and rich genre, despite what people think these days.