LinqPad version that runs in the location of the .Linq file http://share.linqpad.net/e9ne3q.linq

FindConflictingReferences.cs

<Query Kind="Program">
  <Namespace>System.Collections.Generic</Namespace>
  <Namespace>System.IO</Namespace>
  <Namespace>System.Linq</Namespace>
  <Namespace>System.Reflection</Namespace>
</Query>

public class Reference
{
   public AssemblyName Assembly { get; set; }
   public AssemblyName ReferencedAssembly { get; set; }
}
 
public class FindConflictingReferenceFunctions
{
   static public IEnumerable<IGrouping<string, Reference>> FindReferencesWithTheSameShortNameButDiffererntFullNames(List<Reference> references)
   {
       return from reference in references
              group reference by reference.ReferencedAssembly.Name
                  into referenceGroup
                  where referenceGroup.ToList().Select(reference => reference.ReferencedAssembly.FullName).Distinct().Count() > 1
                  select referenceGroup;
   }

   static public List<Reference> GetReferencesFromAllAssemblies(List<Assembly> assemblies)
   {
       var references = new List<Reference>();
       foreach (var assembly in assemblies)
       {
           if (assembly == null)
               continue;
           foreach (var referencedAssembly in assembly.GetReferencedAssemblies())
           {
               references.Add(new Reference
               {
                   Assembly = assembly.GetName(),
                   ReferencedAssembly = referencedAssembly
               });
           }
       }
       return references;
   }

   static public List<Assembly> GetAllAssemblies(string path)
   {
       var files = new List<FileInfo>();
       var directoryToSearch = new DirectoryInfo(path);
       files.AddRange(directoryToSearch.GetFiles("*.dll", SearchOption.AllDirectories));
       files.AddRange(directoryToSearch.GetFiles("*.exe", SearchOption.AllDirectories));
       return files.ConvertAll(file =>
       {
           try
           {
               Assembly asm = Assembly.LoadFile(file.FullName);
               return asm;
           }
           catch (System.BadImageFormatException)
           {
               return null;
           }

       });
   }
}

// Based on https://gist.github.com/brianlow/1553265
   private static void FindConflicts(System.IO.TextWriter output, string path)
   {
       var assemblies = FindConflictingReferenceFunctions.GetAllAssemblies(path);

       var references = FindConflictingReferenceFunctions.GetReferencesFromAllAssemblies(assemblies);

       var groupsOfConflicts = FindConflictingReferenceFunctions.FindReferencesWithTheSameShortNameButDiffererntFullNames(references);

       foreach (var group in groupsOfConflicts)
       {
           output.WriteLine("Possible conflicts for {0}:", group.Key);
           foreach (var reference in group)
           {
               output.WriteLine("{0} references {1}",
                   reference.Assembly.Name.PadRight(25),
                   reference.ReferencedAssembly.FullName);
           }
           output.WriteLine();
       }
   }
 
   static void Main(string[] args)
   {
       var paths = new List<string>();
       
       paths.Add(Path.GetDirectoryName(Util.CurrentQueryPath));

       foreach (string path in paths)
       {
           FindConflicts(System.Console.Out, path);
       }
    }