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Tear Jerker: The Castle of Cagliostro
The end of The Castle of Cagliostro, when Clarisse begs to go with Lupin and embraces him. He's about to hug her back, but forces himself not to, and lets her down gently, almost brotherly, so she can live a better life. That right there? Is the reason I'm an Arsène Lupin III fangirl. I don't care if it isn't technically canon, it's canon for me.
When Zenigata gets back to Interpol HQ to convince his bosses to take down the Count's counterfeiting operation but instead gets buried in the political bullshit of the times, he has to tell his men that they will not deploy to Cagliostro, but will be taken off of the Lupin case pending approval. Unlike in many other cases where he's been relieved of duty or outright fired, he is gracious in defeat. Only his stern, bowed expression tells the audience how crushed he feels.