Originally Junction was the name of several planets. Junctions for the Space Guild. They probably had serial numbers and codes. Long forgotten now. The name was used to refer to mostplanets or planetary objects used for Guild operations, and to a primary center for Guild activity.
In the latter case, this main planet served as the headquarters for the Spacing Guild? and its bank. It was also the location of the only Navigator school. The surface of the planet was almost completely covered with landing fields and repair bays for heighliners.
Junction was also the location of the Navigator's Field, where Guild Navigators who had died were memorialized.
The mysterious Oracle of Infinity was also found there: a clearplaz globe through which the Navigators would "commune."
At least one planet still carry the name. That is the planet described here
Junction has been taken over by the fierce Honored Matres? as a stronghold for their leader, the Great Honored Matre Dama. It's buildings possess what Miles Teg calls "that special Guild flavor ... compounded of Ixian technology and Navigator design — buildings wrapped around space in the most energy-conserving way ... And that permanent grayness to all construction — not silver but as dull as Tleilaxu skin. Chambers and hallways are immense, to accommodate "convocations of Guild Navigators" in their enormous tanks.
Sources: Chapterhouse: Dune?