Hola a todos.
  
Finalmente mi consulta, para generar mi tabla, con los elementos a CERO y ordenados y agrupados como necesito es la siguiente:    
Código MySQL:
Ver original- SELECT-  t_applications.APPLICATION_ID ,-  t_applications.APPLICATION_name_spanish ,-  t_materials.MATERIAL_ID ,-  t_materials.MATERIAL_name_spanish , count(- t_products_materials.PRODUCT_ID )
 
- LEFT JOIN-  t_products_applications  ON-  t_products_applications.APPLICATION_ID  =-  t_applications.APPLICATION_ID  
 
- LEFT JOIN-  t_products_materials  ON-  t_products_materials.PRODUCT_ID  =-  t_products_applications.PRODUCT_ID  
 
- AND-  t_products_materials.MATERIAL_ID  =-  t_materials.MATERIAL_ID  
 
- GROUP BY-  t_applications.APPLICATION_ID ,-  t_applications.APPLICATION_name_spanish ,-  t_materials.MATERIAL_ID ,-  t_materials.MATERIAL_name_spanish  
 
- ORDER BY-  t_applications.APPLICATION_name_spanish  ASC,-  t_materials.MATERIAL_name_spanish  ASC
 
Si le veis alguna manera de optimizarla, no dudéis en decírmelo.  
Saludos.   
Javier