Any show by Tim Minchin. Move-wise, I loved the ever so subtle Sausage Party.

Anything by Todd Solondz tends to be borderline nihilistic. His unique genre of sad comedies is a great source of dark humor. His film Storytelling has one scene in particular that sticks out in my memory as explicitly atheistic.
A rich kid (7 years old or so) is talking to his poor immigrant nanny who is toiling away, scrubbing the floor. He asks her, "Why did your parents have so many children? If they were poor, why didn't they just have one or two?"
She responds, "It was God's will."
He then says, "But do you really believe in God and heaven and hell and angels and all that?"
She takes a short pause, then looks up to him and simply says, "No."

West World

Star Trek

Rick and Morty. It's my absolute favourite show. LOL

I loved that movie Spotlight. I thought it was a great storyline and based on actual events which perhaps maybe opened up a few minds that watched it. I also like Religulous. Funny twist & it exposes a lot.

Star Trek because it never spoke about any Gods as far as I can remember.

Babylon 5

Rapture Palooza is really funny!

The Ledge (2011).

Also, as a portrait of religious hucksterism, even though it doesn't deal specifically with atheism, Elmer Gantry (1960) is hard to beat.

The Sunset Limited, not so much undertones as in you face.