Operating as a company that is subject to Dutch VAT in the EU makes you receive or issue 0% VAT invoices. Is it this simple or not?
If you have a client in the EU to whom you invoice with Dutch VAT, then you can issue a 0% invoice. However, besides the regular invoice requirements, you need to put on the invoice the VAT number of your client as well. Please make sure that the clients provides you with a valid VAT number. You can check the VAT number at this site: http://ec.europa.eu/taxation_customs/vies/
In the VAT return you provide the amount of 0% turnover at question number 3B and you are required to complete another form in which you specify the turnover per VAT number. If then turns out that the VAT number is incorrect, the 0% turnover is denied and you have to either send an invoice for 21% VAT or recalculate the invoice in such a matter that you can pay for the VAT without asking the client for it.
Invoices charged to you at 0% from EU companies such as Skype you report this in the VAT return, you pay 21% VAT to the tax office under number 4b on the VAT form and at the same time you claim back at number 5b the same amount of VAT. It may look like a silly accountancy measure, but if you are a (partly) VAT exempt company in the Netherlands that receives a 0% invoice from an EU company, then the VAT due over this invoice under number 4b needs to be paid, but this cannot be (fully) reclaimed under number 5b.