I'm a beast on atmospheres and drones. The secret is pitch shifting sounds or synths down, and a heavy emphasis on the wet signal of reverb plugins. My favorite is the uhbiks ambience processor! So good, you should invest in the whole uhbiks plugin collection, theres the granuliser too that works really well when automated.
Other way is browsing through some atmosphere presets in any synth and dwiddling with the knobs. And like Jhepz said, I think, turn the filters for some movement. Good way is to layer some of them too, get a drone, make it stereowise very narrow, then add a spacey ambient sound and get it full stereo with any widening plugin. I like to automate the reverb dry/wet knob too in relation with the sound.
I like to give presets some attention, when it comes to dark ambience. Some of them are made to use on higher octaves normally, but they sound great at lower octaves. I like to create a heavy ambience base, and layer some quick squeaks here and there, using panning automation. Also, I'm still training on using granulizers for dark ambience, the results are pretty interesting.
Also, try to use very long notes (16-32 bars), as Elzerk said (when mentioning the term "drones").
You can use some conga loops as well, applying heavy reverb, maybe some phasing. It will give a more "ritualistic" kind of sound, too.
Some proper good responses in here, you'd be wise to listen to them. Something I've been doing lately is (after processing a bit) bounce it back into my DAW on two separate channels, lower the gain a bit on both, pan one more to the left and the other to the right, and offset the timing slightly for the 2nd. Usually for stuff where I want an echo but might want to do some separate effects processing on the duplicate.
Waveform-wise, sines are usually the best way to go, at least for the primary oscillator. In fact take into account how many oscillators your synth has. If it's a single-osc you probably won't get that much for an atmospheric sound or will have to do a lot of processing and mixing down/resampling, which requires even more foresight. FM synthesis usually requires two or (preferably) more oscs to get the most out of, but it can be a great friend for an atmospheric pad.
Like I said, FM synthesis is your friend, it's very useful for those sorts of dark creeping, sorta "metallic" atmospheric sounds, if you use it right. Every synth is different so it just comes down to learning the one you use. I guess some granular synth would be great too, but I haven't tried much of that personally (DarkYsidro probably has more exp there so ask 'em on that).
If you're doing multiple notes (a chord), keep them in the same harmonic/octave range usually* and depending on the type of atmospheric you want possibly try a touch of ring modulation and some light phasing. And of course make sure the stereo signal is "wide enough"; it doesn't need to be 100% (I assume that's usually the case for most atmospheric sounds), but it does need to give the feeling you're in a big space and getting "enveloped" in a canyon, so to speak.
You might want to also detune the original sound in the synth a little, depending on how your synth works, and adjust the pitch for one of the oscillators but keep them in octave (others would refer to "pitch" in this instance as semitone). Try and figure out what your fundamental(s) are w/o having to adjust the octave/transpose range of your synth b/c that'll make getting the sound you're looking for quicker and easier. Get some nice pulse width modulation in there as well but the amount will vary. And if it's what you want, a bit of distortion could work.
I know that sounds like a bunch of shit, but they're just general tips you can take into consideration piecemeal. Don't literally do every single one to try and create an atmospheric sound, b/c some tricks will be unnecessary or even ruin what you're aiming for.
*=sometimes it can be good to have a note or two an octave/ two octaves higher, but again this all comes down to what sound is there. If the notes at those higher octaves are too loud, manually lower them or just cut 'em.
**On reverb, I agree w/ Jesphz and Elzerk; just be careful you don't overdo it!
Lots of advice above that'd i'd give, can only add sample shit from horror movie trailers off youtube etc, stretch dafuk outta them, pitch down, automate verbs/panning/stereo spread/pitch/.. pretty much everything.
One shots with lots of big verbs can be sweet as well!