Choosing my favourite scene ever would be too difficult. So I am just gonna mention Astro Boy related scenes.
My favourite scene from the 80's Astroboy cartoon...? It's probably the deleted scene when Uran sings about religious deities, from the episode "Uran's Quest". I also really like the scene in the final episode when Astro is constantly holding Nikki's hand as she is taken apart, and all that follows it.
I haven't seen much of the 2003 series since it's original Australian air date on CN years back, so I can only mention the manga adaptation. In volume 1, chapter 7; Atom and his friends are playing with a ball and Uran wants to join in, but Uran kicks the ball too hard and accidentally hurts Atom's friends. My favourite scene is the look on Atom's face in response to that when he says "... Uran!!"

He's angry but also looks so silly.
I wish I could see the 60's series, I have a feeling there would be so many good scenes that I couldn't hope to pick a single favourite.