Using the Product Toolbox you can easily identify simple products that are not linked to configurable, grouped or bundle products.
Once installed you will see another menu in the "Catalog" menu that will allow you to detect...
Bundled products with no simple products assigned to them.
Simple products that are not assigned to a Configurable, Grouped or Bundled product. The simple product must also be set to "Not Visible Individually" in order to show here. This is the typical setting for these type of products.