If you want to compare the source code, then using a pretty formatter (e.g. the one in VS) to normalise formatting, you will still need to handle ordering of members and comments etc.
Better might be to use Reflector on compiled assemblies. Select each class, expand its methods (if you want to include the method implementation in the comparison), copy and paste into a text file, and then compare the text files.
This should eliminate all non-significant (i.e. not in the assembly) details.
(Note, there might be a Reflector plugin to do this directly.)