I recently ran across a blurb in the October issue of Construction Concrete that talked about the effects of pet feces and urine on concrete. The smell apparently comes from bacteria growth within the matrix.
The solution is to wash the concrete throughly and apply a product like StableCrete. StableCrete is absorbed into the concrete and reacts with the alkali and lime forming solids inside. This creates a waterproof barrier and prevents any other contamination.
If the concrete is really bad with contaminants, there might be material on the surface after the first coat. This is material that has been pushed to the surface by StableCrete. Just wash the surface again and apply a second coat.