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!