So, one thing I've been wondering about recording/producing in general is ambient noises.
What makes them?

Take for example, Frances the Mute by the Mars Volta. That album is a masterpiece production-wise (and music-wise for that matter).

What are they using to make all those weird sounds? Is it just synths put through a bunch of different effects pedals?
I'ld say both.
And a good use of reverb and delays.
Mars Volta uses a lot of different stuff from synths to talk boxes to vocoders to a crazy effects pedals rig. Its not really tough to create ambient sounds.
Take a synth, modulate it a bit. Throw in a good reverb and you've got an ambient sound!
Or if you wanna make it more complex, throw in a delay line. Adjust them to trigger at slightly different times. Adjust the feedback, pan one left and the other one right, the sound will bounce between the two delays giving the cool effect of the delayed sound bouncing between the left n right.
You could do exactly the same thing with a guitar too. Take a guitar, plug it into a delay line, throw on a reverb and you've got ambient sounds! Or to play around with the sound more, add a digital whammy to the sound to create more movement.