Rick,
I have taught joint design workshops for the Guild. There is not yet a truly "one stop shopping" reference on joint design. In putting together the Guild courses, I drew from a number of sources, such as the NAtional Design Specifications for wood strebgth, some structural engineering texts, texts on timber design (mostly bolted connections), and various articles.
I don't know your background, but It would appear that you can determine the loads that the joints must resist. It has been my experience that the maximum loading on most joints comes from some combination of gravity load (snow, dead weight, ...) and horizontal live load (Wind, earthquake). It is the horizontal portion of loading that presents the most difficulty in determining the joint loading. Good results rely on a proper structural analysis of the frame as an assembly.
Good joint design depends on good knowledge of the loads the individual timbers are bringinh to the joint.