Graphviz is extremely powerful and I'd be surprised to discover that it doesn't do what you need. It only generates the positions of nodes that aren't already specified so if you need fine tuning then you can run it to get a basic graph, then fine tune it, and then it'll respect your fine tuning. Also, it comes with an interactive program called dotty which can be used to alter the graphs visually.

One should also distinguish between generating graphs and rendering them. I use graphviz to generate graphs, but don't use it for rendering. For that, if PGF/TikZ can't do it then I'm not interested! PGF/TikZ is absolutely fantastic and has consigned xy.sty, xfig, and all the other stuff that I used to use to the rubbish bin [trash can]. Even for commutative diagrams in category theory!