Spacing in a large graph

I am trying to use dot for visualising web logs, but at the quantity of nodes I'm dealing with, it doesn't seem to space them correctly. Could anyone suggest how to improve readability?

The thing I would most like to modify is the first 'app' column. In my attempt (http://i.imgur.com/FGsoSHK.png), the user and app columns are perfectly aligned, where I would like them like this test I did (http://i.imgur.com/Wff0zt0.png), to be more spaced out.

Also, I notice that the top and bottom halves of good.png are quite different, even though the specification of good.png was symmetrical. Why might this be?

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