A cloud was a collection of moisture in the atmosphere. They were the source of rain.
According to a diagram used by the Spy Master, ash clouds could come from volcanos. (TV: The Power of the Doctor)
The Ethereals were turned into living clouds by the Baggolts. The First Doctor, finding it odd that the clouds could exist in a thin atmosphere and move despite there being no wind, tried to take a sample of one, but it captured him instead. (PROSE: The Cloud Exiles)
In 1974, the Zircon attempted to wipe out the Earth with a poison cloud. They were stopped by either the Third Doctor and Sarah Jane Smith or the Fourth Doctor and Joan Brown. (COMIC: Doomcloud)
One day whilst in his village's market, Moop noticed that the clouds were making strange shapes until a face appeared in them. It claimed to be the creator of Moop's people and asked for a tribute. Moop gave the "god" some of his Grunt. (PROSE: The Tomorrow Windows)
After losing his companions and parents-in-law, Rory Williams and Amy Pond, the Eleventh Doctor parked his TARDIS in or before 1892, atop a cloud, high above London. A staircase provided the Doctor a means of inconspicuous entry access to and egress from the surface, while assuring him solitude. (TV: The Snowmen)
In the early 21st century, flying Cybermen led by Missy took to the skies and created clouds of cyber-pollen above Earth's graveyards. These clouds then rained upon the graves, recruiting the dead into a new Cyberman army. When control of the Cyberman army went to the hands of the recently-converted Danny Pink, he ordered all Cybermen to return to the clouds and self-destruct, destroying themselves and the clouds. (TV: Death in Heaven)
After "the company" had constructed a second sun, Kromon's clouds dispersed. (AUDIO: The Creed of the Kromon)
On one planet, what appeared to be an unusual cloud turned out to be an echo across time. (PROSE: Follow the Phantoms)
The Entity, in its domain, was a "formless black cloud that flowed and coalesced" which throbbed with a "terrible passion"; it personified pure evil. (PROSE: Games [+]Warwick Gray, Brief Encounters (Marvel Comics UK, 1992). Page 22.)