I'm having trouble figuring out how my characters joints should be modeled, particularly the shoulder, so that when he is deformed with bones in animation it looks natural and less like hes just had his shoulder bruttaly dislocated by a pair of invisible-sledgehammer-wielding-texan-flying-oilbarons.

The real trick lies in weighting the vertices correctly for each bone connected to the joint. It's always been a lot of trial and error for me, though :-\