Code

// group the nodes
Dictionary<Color, List<DiagramNode>> sortedNodes = new Dictionary<Color, List<DiagramNode>>();
foreach (DiagramNode node in diagram.Nodes)
{
	Color key = ((SolidBrush)node.Brush).Color;
	if (!sortedNodes.ContainsKey(key))
		sortedNodes[key] = new List<DiagramNode>();
	sortedNodes[key].Add(node);
}

// arrange in rows
float dist = 20;
float y = 10;
foreach (Color key in sortedNodes.Keys)
{
	float x = 10;
	float rowHeight = 0;
	foreach (DiagramNode node in sortedNodes[key])
	{
		RectangleF r = node.Bounds;
		r.Location = new PointF(x, y);
		node.Bounds = r;
		x += r.Width + dist;
		rowHeight = Math.Max(rowHeight, r.Height);
	}
	y += rowHeight + dist;
}

diagram.RouteAllLinks();