To get the vertex coordinates for graph g, defined below:
PropertyValue[{g, #}, VertexCoordinates] & /@ Range[7]
e.g.
{{2.32379, 0.}, {2.32379, 0.774597}, {1.54919, 1.54919}, {1.54919,
0.}, {0.774597, 0.}, {0.774597, 0.774597}, {0., 0.}}
To Animate, without moving vertices....
Here's a rough overview of how you might approach the problem using highlights. You don't need to move the vertices. You can simply fill in the graph step by step. We'll build the graph in three steps and then play it backwards. You can add the highlights and additional steps that suit you.
Begin by making the graph you want to end with:
edges = {DirectedEdge[7, 6], DirectedEdge[5, 6], DirectedEdge[4, 6], DirectedEdge[6, 3], DirectedEdge[2, 3], DirectedEdge[1, 2]};
g = Graph[edges, GraphStyle -> "VintageDiagram", GraphLayout -> "LayeredDrawing" ]

Next, make the next to final drawing of the graph:
g1 = Graph[edges, GraphStyle -> "VintageDiagram", GraphLayout -> "LayeredDrawing",
GraphHighlight -> Join[{3, 6}, {DirectedEdge[6, 3]}],
GraphHighlightStyle -> "DehighlightFade" ]

Now let's jump to the first step, where there are two connected components. They need to be in the proper place so they won't have to move later.
g2 = Graph[edges, GraphStyle -> "VintageDiagram", GraphLayout -> "LayeredDrawing",
GraphHighlight -> Join[Range[7], Complement[edges, {DirectedEdge[6, 3]}]],
GraphHighlightStyle -> "DehighlightHide" ]
Setting the GraphHighlightStyle to DehighlightHide allows you to hide parts of the graph (the edge from vertex 6 to vertex 3).

In the animation you will want to display them in reverse order:

Here's the ListAnimate code for showing the three frames we made:
ListAnimate[{g2, g1, g}]

With additional frames you could assemble the graph, vertex by vertex, edge by edge, using the highlights of your choosing.
ListAnimate. – b.gatessucks Oct 10 '12 at 7:58Graphobject, I could do it easily, butLayeredGraphPlotreturns aGraphicsobject rather than aGraph! – Mohsen Oct 10 '12 at 8:20HighlightGraphtogether with Manipulate or (as b.gatessucks mentioned) ListAnimate. – David Carraher Oct 10 '12 at 8:22