Sort entries in a category or entries field? I have a Products Section and a Product Category Structure Section
In Products there is an Entries Field where the Category is selected from the Product Category section.

Is it possible to sort the products per category manually?

I see with the ManytoMany Plugin - https://github.com/page-8/craft-manytomany
You can display the products which appear in each Category and the Custom Ordering of the second Relationship is in the pipeline which would probably work but not available yet.

Is there any other option?
To order the products you'd make the Products section into a structure and display the category you were sorting by in the listing as a table column.

You can then re-order all products to be in category order (using the table column), then re-order each product for each category. 

You can then output each product grouped by category with something along the lines of:

{% for cat in categories %}

  {% set products = products.relatedTo( cat ) %}

  {% for product in products %}

    {{ product.title }}

  {% endfor %}

{% endfor %}