There is currently no way to assign a useful name to junctions in a workspace. I have workspaces with dozens of junctions, and they are all named "Junction_1", "Junction_2", etc. When collapsing bookmarks and adding custom labels to each input/output, and a junction is one or more of the inputs or outputs, it can be difficult to figure out which junction is which without repeatedly opening and collapsing the bookmarks. It is also challenging to connect to/from junctions in the Feature Type Connections window without knowing which junction is which.
On a related note, being able to browse the usefully-named junctions in the Navigator would also be very helpful.
