Not knowing what type of data you're representing through these nodes, I'll assume that typically you'll be browsing the nodes by looking from the parents to their children. (If the nodes have some sort of "meaning" associated with them, a better metaphor might be appropriate...)

In that case, the most logical thing to me is a node->subnode explorer style (like you were doing) with multi-parent nodes listed under their respective parents (perhaps with a identifier or something that indicated that they came from a complex family.)

Not particularly earth shattering, but that's what makes sense to me. (Just like entering a directory with soft links in it... makes sense to see the soft links in that directory, even if they exist in multiple directories.)