One of the most common requests we get for OmniGraphSketcher is to support multiple y-scales overlaid on the same graph, to make it possible to plot several different types of related data on the same chart. Some people call this approach “dual y-axes” because graphs of this type tend to put vertical axes on both sides of the graph area. For a while now we've been debating whether or not this is a good idea.
We've now posted an article with our thoughts on the matter.
Our main conclusion was that overlaying data with disparate scales saves space, but it makes the data significantly harder to interpret. The dual axes “duel” for your attention. So instead of overlaying scales, we recommend using a set of multiple graphs, aligned along their common axis. Graph Sketcher does not have a built-in option for this, but you can easily Copy As Image with each graph and paste into OmniGraffle or another program with layout capabilities.
Read the article for more details, and if you have a graph with overlaid scales that you think is more effective than its separated-and-aligned counterpart, please let us know—we still have an open mind about it.