They are such named after the dozens of spherical objects they created in the area of the Milky Way Galaxy known as the Delphic Expanse. The spheres are actually highly advanced mechanisms capable of altering the properties of time and space, creating spatial anomalies that will slowly convert the Delphic Expanse into a realm which should be inhabitable by the Builders.
When exposed to our natural, unaltered space, the Builders' bodies quickly decay. Regardless, they are interested in colonizing our dimension using the spheres to make it suitable for them, and have organized a large hostile invasion by the time of the 26th century.
The Sphere Builders either don't perceive time in a linear fashion; or have mastered technology that allows them not only to travel through time but to predict the multiple long-term effects of timeline alterations. They are one of the main faction of the conflict that became known as the Temporal Cold War, which is related in some way to the aforementioned 26th century invasion. In the distant future, many political forces have became capable of traveling to the past; including the Builders, the United Federation of Planets and the Na'kuhl; and all have traveled back in time to attempt to alter history in their benefit, in some cases creating alternative timelines altogether.
The Sphere Builders were responsible for re-configuring the Delphic Expanse area into a zone of strange and unexplained phenomena; akin to a cosmic Bermuda Triangle; and have thus became worshiped as gods to many of the Expanse's native species. The Xindi refer to them as the Guardians. To the Triannons, they are the Makers. During the Temporal Cold War, one of the Sphere Builder's main plans to sabotage the formation of the Federation, was to incite the Xindi to attack Earth in the 22nd century, when Humans were just beginning to integrate themselves in the galactic community. They offered advanced weaponry to the Xindi and incited their anger by "revealing" to them that Humans were destined to destroy the Xindi race in the future, if the Xindi didn't attack first. That plan ultimately failed, though, and it is hinted that Humans and Xindi would even become allies by the time of the Builders' invasion; which was successfully repelled by the 26th century Federation, forcing the aliens back to their native dimension.