The movie Love Actually (2003) has a rather complex relationship map but not really when it comes to gaming. I ran one of my Aftermath! games with a pretty complex map, linking together a large number of organizations that included the player characters and NPCs within those organizations. As the campaign wound along, the map changed quite a bit - some groups were wiped out by other groups, others formed alliances with each other, and others still pursued their own agendas even amidst the chaos of the post-apocalyptic landscape.
The Smallville RPG has relationship maps built right into the character creation. Perhaps that's the way to start - with character creation, instead of kludging it on later.