John, turn on the light.
This is an imperative. You're telling the listener what to do. In imperatives, the subject is generally taken as an implied "you":
you turn on the light.
The verb doesn't change form to agree with you, though; in an imperative the verb always appears in its plain form, which is the same form of the verb as the infinitive:
you be careful.
As you can see, if we change the verb, we end up with be, not are. So no matter what, it won't have the -s you're asking about on the end.
John isn't the subject, so the verb doesn't change form to agree with it. Instead, John is something called a "vocative"—basically, you're saying his name because you're talking to him. It doesn't have to go at the beginning of the sentence, either:
You turn on the light, John.
The same is true of your other examples:
you eat your breakfast.
you wait a minute please.
And again, the names are vocatives and not subjects. We can move them to the end:
You eat your breakfast, Stig.
You wait a minute please, Maya.
And the verb stays the same.