What is the best way to compare the results of different Examine3D files?

Use DStress, which is a utility for looking at differential stresses between two models for the purpose of examining changes in displacement and stress due to staged excavation.  The values are computed by subtracting the File1 results from File2.  The results file created by DStress is a text file that can be easily read.  To see the format, you can look at one of the .res files created by the Examine3D compute engine.

You can also always manually look at the stresses and displacements on specific cutting planes.