It took me some time to make the graph below look like it does right now, and I'm almost satisfied. The one thing that still bothers me is that the connection between D and B should be above all nodes for the sake of aesthetics.
The funny thing is, that supplying the ports for the edge doesn't impress dot which just makes the edge cross the connected nodes.
Do you have an idea on how to avoid this?

digraph {
graph [splines=ortho, nodesep=0.2, fontname="DejaVu Sans", rankdir=LR]
node [shape=box, fontsize=8]
edge [arrowsize=0.5]
subgraph cluster {
style=invis;
A -> B -> C;
A -> B -> C;
A -> B -> C -> D;
D -> E;
D:nw -> B:ne;
}
{
D -> F -> { C; E };
}
}
PS: You need the latest Graphviz version in order to get orthogonal edges.

Currently, the routing does not handle ports or, in dot, edge labelswhich may be the cause of the problem. I thought inserting an invisible node between D and B might help resolve the problem, but I tried various ways of doing that and none of them improved matters. I'll think further about this. - Simon