ディレクトリ内のdllをループするだけでよいようです。
また、既に読み込まれているアセンブリを読み込まないようにする必要があります。
例えば:
  string bin = "c:\YourBin";
    DirectoryInfo oDirectoryInfo = new DirectoryInfo( bin );
    //Check the directory exists
    if ( oDirectoryInfo.Exists )
    {
       //Foreach Assembly with dll as the extension
       foreach ( FileInfo oFileInfo in oDirectoryInfo.GetFiles( "*.dll", SearchOption.AllDirectories ) )
       {
                        Assembly tempAssembly = null;
                        //Before loading the assembly, check all current loaded assemblies in case talready loaded
                        //has already been loaded as a reference to another assembly
                        //Loading the assembly twice can cause major issues
                        foreach ( Assembly loadedAssembly in AppDomain.CurrentDomain.GetAssemblies() )
                        {
                            //Check the assembly is not dynamically generated as we are not interested in these
                            if ( loadedAssembly.ManifestModule.GetType().Namespace != "System.Reflection.Emit" )
                            {
                                //Get the loaded assembly filename
                                string sLoadedFilename =
                                    loadedAssembly.CodeBase.Substring( loadedAssembly.CodeBase.LastIndexOf( '/' ) + 1 );
                                //If the filenames match, set the assembly to the one that is already loaded
                                if ( sLoadedFilename.ToUpper() == oFileInfo.Name.ToUpper() )
                                {
                                    tempAssembly = loadedAssembly;
                                    break;
                                }
                            }
                        }
                        //If the assembly is not aleady loaded, load it manually
                        if ( tempAssembly == null )
                        {
                            tempAssembly = Assembly.LoadFile( oFileInfo.FullName );
                        }
                        Assembly a = tempAssembly;
       }
     }