If I have a junction box where there are splices from several circuits, do I connect all ground wires from all circuits together in one bundle or do I do that for each circuit within the junction box?
You connect all the grounds together with a ground crimp connector. A wire nut is not sufficient to meet code.
And then if the box is metal, you connect the crimped bundle to the box. Leave one of the ground wires longer than the others, sticking through the crimp connector, and attach that one to the box.