I've been working in a company run and owned by DH and I for the last 16 years.
I want to apply for a management job in a school. The application form states that one of the referees MUST be your present or most recent employer. Now technically I guess that would be DH, but I'm sure that wouldn't be acceptable.
You could put a client, depending on what type of business it is, or you could write that you have been working for your own company for 16 years and would be happy to discuss an appropriate referee with them, or you could ring and ask what they'd like you to do.