I'd like to take a simple graphviz input file (or alternatively something as simple as the X -> Y notation) and have a graph where I can reorganize the positioning of the nodes without having to specify the coordinates by hand. Is there there a way to do this?
If you run graphviz in SVG output mode, you'll get an SVG file, which you can then edit easily (e.g., with Inkscape).
dot -Tsvg foo.dot > foo.svg
or neato, or whatever.
-Tps (PostScript), and
-Tdia (dia, Linux/GTK diagraming tool) may also work, depending on what software you have available. A complete list of output formats is available.
Of course, the point of graphviz is that you don't have to lay it out by hand... have you looked at some of the graphviz options? They may alleviate whatever problem you're having.
Depending on your needs for editing you can do:
neato -Tsvg pollo.graph > pollo.svg
And then you can edit the file with inkscape, for instance.
The problem is thatt it doesn't maintain connections between objects.