Currently you can just give a name to a connection:
But I would like to see the ability to apply additional formatting to a connection, most importantly color.
Currently you can click on an individual tool and the incoming and outgoing connections will be color coded, but when working in a complicated workflow color coding would make understanding the connections easier, without the need to click on individual tools.
Just like the ability the right click on a tool and say "Make (incoming / outgoing) connections wireless" you should be able to right click on a tool and specify the formatting of all incoming or outgoing connections.