I’ll second Freakwater and recommend the album “Old Paint”
also check out…
The Handsome Family - Through The Trees or Milk & Scissors (it doesn’t get darker than this)
Neko Case - Blacklisted
Trailer Bride - Hope is a Thing With Feathers
Bughouse Five - Dark Days Passing
Old Reliable - The Gradual Moment
Devil In A Woodpile - Division Street
Or just check out Bloodshot Records
A couple of personal favorites:
“Long Black Veil” - very spooky. Done by Johnny Cash, for one.
“The Banks Of The Ohio” - A good murder story - various artists.
I also ran across a singer named Shawn Philips whose song “The Ballad of Casey Dese” has spooked me out since I was fifteen. It’s on the “Second Coming” album.
Speaking of murder ballads, BR-49 does a cover of the murder ballad “Knoxville Girl,” though their style is more honky-tonk than traditional.
Yeah, and bluegrass is probably too perky for Pookah. But a couple of the disks from Harry Smith and the Child Ballads (of course, there’s lots of crossover) oughta be just the ticket, chock full of murder and misery as they are. Can’t hardly be a Child Ballad if nobody dies. Or gets knocked up. Or both. Acapella Goth, so to speak. You can read many and hear annoying MIDI versions of them here.
[aside]
I, and you, know how much more knowledgeable the rest of you are than I so it’s probably no surprise that I was surprised to learn, after years of hearing and hearing about the Child Ballads, that Child was an American.
[/aside]
They were mentioned previously, but I’ll cast a strong vote for the Original Carter Family. Also mentioned, Charlie Poole & The North Carolina Ramblers show some jauntiness but lots of darkness, too.
The New Lost City Ramblers were one of the first “modern” groups to do old-timey. They also recorded with Hazel Dickens & Alice Gerrard as the Strange Creek Singers–another oldie now available again. (On Amazon, I just noticed more music by Hazel & Alice–truly haunting.)
The other side of modern old-timey is represented by the Holy Modal Rounders. True weirdos, their first two LP’s (now available in a CD set) did capture the spirit of the old singers. (Lots of them were weirdos, too.) Later stuff from the Rounders got less acoustic & lots weirder.
The Red Clay Ramblers played fine old-timey but branched out. Roots tunes from the British Isles, classic bluegrass, ragtime, folk-rock, etc. Just had to mention them because they’re so fine. Some of their music in more modern styles still had a touch of darkness & mystery.
I think I’ve got an idea of what you’re looking for … Appalachian folk ballads heavily influenced by (or taken straight from) their English, Scottish and Irish ancestry? About dead children, dying women, and gals warning other gals to be wary of a guy who’ll surely break their heart and lead 'em to naught but ruin, sorrow, a baby and/or suicide? That sorta thing? 
If so, I have two related recommendations. First, you can rent or buy the movie Songcatcher, with Janet McTeer, Aiden Quinn and Pat Carroll. It’s about a university musicologist (McTeer) in 1906 travelling to a rural, isolated community on an Appalachia mountain in order to hear, record and notate the local folk music (which until then has gone unpublished).
Naturally the plot follows some of cliches of the typical “stuffy city type meets insular country folks and learns their ways while edumacating them” genre, but I think it is a better quality than most films that fit into this category. Interesting character actors and evocative settings bump this up a notch, IMO. Best of all, throughout the movie you hear some haunting, catchy traditional music sung by the actors, mostly a capella. And you learn a bit about the culture that put so much heart into their music.
Second, there are two soundtracks related to the film that I definitely recommend. There’s the official soundtrack, which includes both clips of songs as sung in the movie as well as complete versions recorded by singers such as Emmylou Harris, Roseanne Cash and Dolly Parton.
Then there’s the follow-up, Songcatcher II: The Tradition that Inspired the Movie, which captures live performances from a 1960s Newport folk festival. Less polished than the other recording, but more authentic and gritty. The website I’ve linked to has some good notes about the background and artists, as well as brief audio clips.
Hope this helps! After seeing the movie on HBO I fell in love with the music and sought it out. I love dark stuff too! 
(Smilie usage notwthstanding.)
Wow. What a great response to my question. This is going to keep me listening (and bankrupted) for a good while. I’m once again going to fall foul of the “no thank you posts” rule and post a big THANK YOU to all who posted their recommendations. What I’m going to do is print out the lot and have a look at it every time I feel like/can afford to buy CD’s as there are now way too many tasty sounding things to check it all out at once.