There are several types of events that happen in deep space that space travelers refer to as storms.  This is a brief description of the several types of space storms.

Gamma Ray Burst

Big, cosmic events can release huge amounts of energy in the form of gamma rays.  Even the best shielding can do little to protect life-forms from the full power of a gamma ray burst.  Fortunately, the vast distances to such events means that most of that energy has usually dispersed by the time it gets near inhabited worlds.  Close proximity to such events is not advised. 

Gravitational Waves

These are caused by large-scale cosmic events, such as black holes colliding.  The magnitude of the distortion in space-time caused by these waves is usually small enough that it isn't noticeable in normal space, but ships in hyperspace can be thrown off course substantially, or even broken up by the distortions.  Gravitational waves caused at least one colony ship to crash on New Albuquerque.

Meteor Shower

This happens when a ship passes through an area containing a number of small asteroids, or alternately when a group of asteroids strike a planet or other habitation.  The main threat of this type of storm comes from the relative velocity between the ship and the asteroids.  This type of event can damage or destroy a ship in space.  Planets with substantial atmospheres generally have the asteroids burn up before they strike the ground.

Neutronium Burst

Sometimes, even neutron stars are destroyed.  They might crash into other neutron stars, or get engulfed by a black hole.  When this happens, fragments of hyperdense neutronium can be released in what is known as a Neutronium Burst.  The high density of these fragments makes them far more dangerous than asteroids. 

Stellar Flares

Most stars have events of this type, at least occasionally.  Stellar flares cause plumes of electrically charged plasma to erupt through space.  If they strike a planet or a ship, Stellar Flares can disrupt communications, take out power systems and destroy electronics.

Unstable Wormholes

The fabric of space is not as stable as it might seem.  Wormholes to distant places and times, (and even even parallel universes) occasionally appear for unknown reasons, and at unpredictable places and times.  These wormholes can flash in and out of existence in an instant, or linger for years, providing access to distant places and times.  General Zarlok used such a wormhole to end the 1,000 Years War.