In the iPod version, they don't serve much of a purpose except for the mini-game Ooga Jump where Pygmies jump on different types of clouds to reach a higher score. If the clouds are swiped to one side they will become Storm Clouds.
In the online version, normal white clouds serve as much purpose as they do in the iPod version but some players like them so that the backround looks more cheery than having thunder clouds all the time.
They are present on Earth and don't have any purpose in the sequel except to float around. On Uranus, their are floating white clouds by they appear somewhat cylindrical. On Mercury, the floating white clouds are yellow.