As Mark asked, it really depends on which clouds you are asking about. Sky Editor, Realistic Sky, or the volumetric clouds.

All of them are animatable. The two sky editors are pretty straight forward. The Volumetric clouds require some poking around in the Master Object in the sequencer. From there you will find most of the attributes from the cloud editor dialog. Just create keyframes by adjusting the values at different times on the timeline.

Donnie