These clouds are called coronal mass ejections or CME's. They are sometimes associated with flares or prominences, but also occur alone. The number of CME's varies with the solar cycle, going from about 1 a day at solar minimum, up to 2 or 3 per day at solar maximum. CME's, like flares, disrupt the flow of the solar wind, and can cause wide-spread damage on Earth. Research is ongoing to understand the way in which CME's form, with the hope of being able to predict them.
Space weather is of interest to communications and power companies, as well as the military.
If CME's could be anticipated, it would be possible to shut-down satellites and minimize damage. Here is an MPEG animation of a coronal mass ejection. The source of the sun's activity is believed to be the Solar Magnetic Field which can be seen in this 3-D visualization . The magnetic field structure of the Sun is very complex. Field lines are dragged and twisted by the Sun's differential rotation.