This is an etiquette question that comes up most frequently in another tipping situation, the beauty salon -- where the owner is very often the one providing the customer's service herself or himself. Modern etiquette is to tip the salon owner as you would a non-owner, although, like everything in tipping, the issue stirs controversy.
Here's how the situation lays out in a restaurant.In many countries, and particularly the United States, gratuities account for most if not all of a server's compensation. Most people understand that if they fail to tip their server, that person is not getting paid for the work they've performed, no matter how inadequate or flawed that work happened to be. When the owner is your server, it seems that he or she is already making money off of your meal -- and so if you don't tip, it's not like you're not depriving the owner of a wage.
But etiquette requires that you tip the restaurant's owner as you normally would. Here's why:A waiter or waitress provides you with a service, and when you calculate a tip you take into account the amount of the bill, cultural norms for the area, and a few percentage points of wiggle room for quality of service.
Notice that the server's background or financial situation doesn't enter into your calculation -- a tip isn't like a needs-based scholarship. You wouldn't tip a waitress less if she happened to be an heiress, and you'd probably get fairly annoyed if a waiter shared a hard luck story and implored you for greater generosity.
Like it or not, restaurants that don't have a service charge have factored a gratuity into their pricing. You're not entitled to give yourself a discount if the owner waits on your table.
If you're still not convinced that you should tip the owner, it should be easier to decide to tip the owner's family member, whether it's a spouse, child, cousin, aunt. You have no idea what the financial arrangements are inside the owner's family, and in any event, a customer is not in the position to decide what sort of compensation a person should get for working in their family's business.
Of course, an owner is free to decline a tip. But if it's not mentioned, simply calculate your tip as you normally would. And if the whole concept is really bugging you, tip at the bottom of your range.