When you say someone has nodded in agreement it is meant that they are lowering and raising their head to signify their agreeance without needing to say anything.
There is a more subtle version of this, quite common in film, where Character A is asked a question and Character B responds by essentially blinking in agreement or by nodding with their eyes/eyelids. They do not move their head, and they may say something, but usually when they don't it used to deliberately not make it 100% clear to the audience what Character B's intentions are. I can't think of a specific example but I have seen it especially in high tension situations when a group of characters are trying to determine what side of the fence each person is, or during interrogation scenes.
Example 1 (bold part is what needs replacing):
After the meeting, Paul walks straight up to John, deliberately menacing.
"So I hear that you're going to fire Tom?" demands Paul.
John nods with his eyes, wary of the attention from the other colleagues in the room.
"Was that a yes then?"
John nods with his eyes again, "We should talk about this privately, Paul. So we don't disturb the other workers."
"You really are a coward John!"
Example 2 (bold part is what needs replacing):
"Paul, were you or were you not at the suspects house 2 nights ago?" asks Officer John.
Paul nods with his eyes.
"Was that a yes? Please verbally confirm for the audio recording."
Paul again nods with his eyes, answering John but not letting his answer be recorded.
"Dammit, you answer me Paul!"