A cloud was a visible mass of water vapor or frozen crystals floating in the atmosphere above the surface of a planet or other planetary body. The term also informally referred a mass of matter drawn together by gravity that resembled a cloud, such as billowing smoke. For example, nebulae were sometimes known as interstellar dust clouds. (TOS: "The Immunity Syndrome")
Clouds were responsible for producing precipitation; a common consequence of water vapor clouds on planets was the meteorological phenomenon known as rain or snow. Storms, lightning, and thunder were also associated with clouds.
One type of cloud was the cumulonimbus. Low-level clouds very near or at a planet's surface were called fog.
Fighter jets sometimes flew under the clouds. (TOS: "Tomorrow is Yesterday")
Watching clouds was a pastime enjoyed by some. In 2267, Spock and Leila Kalomi watched the clouds on Omicron Ceti III. He commented that one looked like a dragon. It was something he'd never taken the time to do before. (TOS: "This Side of Paradise")
Clouds also appeared on other planets, for example, the planet housing the Vulcan monastery at P'Jem and Angel I. (ENT: "The Andorian Incident"; TNG: "Angel One")
The holographic program having Natasha Yar speak to her friends following her death included several clouds (TNG: "Skin Of Evil") as well as the holographic recreation of Café des Artistes in Paris on Earth. (TNG: "We'll Always Have Paris")
In 2371, after the USS Voyager landed on a planet in the Delta Quadrant, Captain Kathryn Janeway watched the clouds through the windows of her ready room. (VOY: "The 37's")
When Vexilon, the environmental control computer of Corazonia, malfunctioned during an operating system update in 2381, the clouds over the Dyson ring's interior surface froze solid and fell to the ground. (LD: "In the Cradle of Vexilon")