Normally just water vapour. However, sometimes pollution causes acid rain – this is where sulphur dioxide and nitrogen dioxide mixes with cloud water vapour or rainwater and makes acid, which damages trees and buildings. Volcanos can also produce clouds of ash, but these aren’t like normal clouds! Equally, you get clouds in space, which are made of very cold hydrogen – this is where stars form, because the clouds are very dense and can eventually make dense enough gas to make stars.
It’s been shown that clouds that form rain form around tiny bits of dust in the atmosphere, this is the first little hold a water molecule gets and then all it’s buddies can join on! It’s mostly water vapour, but to help form the tiny droplets usually you need something to help the process along. It is possible to “seed clouds” http://en.wikipedia.org/wiki/Cloud_seeding
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