They all emphasize different things and thus are usually useful for different graphs. dot has a hierarchical layout, circo arranges nodes on circles, neato uses force-directed layout, etc. Of course they're not going to be all useful for the same graph. When preparing our own layout styles demo [1] we took care in crafting a graph for each layout and also explaining a bit on which layouts are good for which use case. There isn't really a magic layout algorithm that works on every graph to make it clearer. We have something built into our graph editor that analyses the graph and picks a layout that might be suitable, but that still errs often enough since it can't know about labels or what the graph actually represents.

[1] http://live.yworks.com/yfiles-for-html/2.0/layout/layoutstyl...