The horse's head scene
The scene where studio boss Jack Woltz realises that he is outmatched by the Godfather, despite àll his power in Hollywood. His refusal to cast Johnny Fontane in his war movie results in an amazing act of intimidation.
When Tom Hagen is being shown around by Woltz on his estate, Tom would have noted how much Woltz loved his race horse Khartoum. It was a prized possession. The idea to take away Woltz's pride and joy must have started there. Tom would have reported that back to Vito Corleone who would have then given the order.