Beneath The Planet Of The Apes
(AstroChuck is gonna be upset I got that one first)

When the Wind Blows
Dr. Strangelove

Les Miserables

Seeking a Friend for the End of the World

Melancholia

On The Beach(1959_film)

Devilman.
Neon Genesis Evangelion.

There is Night of the Living Dead. Although the world is destroyed but no one makes it out of the house alive. There are a few like Invasion of the Body Snatchers, where they beat the invaders but at the end they show some pods got through to start again. Maybe not exactly what you’re looking for but food for thought.

This is kind of the ultimate spoiler thread.

Where everybody dies? The only two I can think of are “based on true story” films, which stick in my mind for exactly that reason – the infuriating, “How can this possibly be a true story if no one lived to tell it??”

The Perfect Storm
Open Water

The second one probably doesn’t qualify as a proper disaster movie (too few deaths).

Oh! I just thought of one – The Cassandra Crossing. If I recall correctly, the whole point of the ending was that everyone on the train had to die, so that they wouldn’t spread the disease.

Fail Safe

Uh, @anniereborn Les Miserables isn’t a disaster movie (even though it feels like one in a place or two.) Also, the newly married Mario & Cosette survive in the end.

@sahID Yes, I know. It was supposed to be a funny. As in theater circles the tag line is
“Les Mis: Everbody Dies”

“When Worlds Collide” comes close.
“Ladybug, Ladybug” – Le boom.

Knowing… only two survivers

@kritiper – I disagree about WWC – earth is destroyed but they do move to Bronson Beta and start to rebuild civilization.

I’m going to make it a point to follow up on many of the other suggestions.

(No, Les Mis is not a disaster movie)

Seems to me the 1978 version of Invasion of the Body Snatchers qualifies (and is well done).

The Alien series seems to be eventually Game Over for everyone, if you watch enough sequels and don’t count xenomorph reanimation as survival. Though after Aliens, the sequels get pretty bad… I prefer to pretend that was the last in the story…

… not sure those are really disaster films though, per se.

Oh! Here’s a good one, though it’s a spoiler to say so: Perfect Sense.

Also (end of world and/or humans):

Knowing (though perhaps not exactly in genre, does destroy Earth with a natural disaster)

The Day the Earth Caught Fire is left ambiguous whether we all die or not.

4:44 Last Day on Earth

Seeking a Friend for the End of the World

Of more limited scope, but killing everyone in the film:

The Bedford Incident

And

Cloverfield

Cabin in the Woods

Any Steve Martin film, each one a disaster & every single joke dies on its feet.

Last Man on Earth, the first film based on I am Legend, stays true to the novel rather than giving it that Will Smith feel-good happy horseshit non sequitor of an ending.

Took me a bit to find this gem we loved in my childhood:
The World, The Flesh, and the Devil

Along the way I found:
The Last Man on Earth (1964)
On the Beach (1959)
A Boy and His Dog (1975)

See more here if you like, but I thought those fit your question best.

Edit:
I’m not certain that I have seen “The World, The Flesh & The Devil”. I remember watching the first part with the devastation and initial contact between Harry Belafonte and Inger Stevens, but not the character Mel Ferrer played. Either I fell asleep as a child, or was put to bed.
Fantastic! I’m looking to purchase a DVD now.

I cannot remember which incarnation of “Final Destination” [SPOILER ALERT] that took place in a mall with an exploding movie theater, but that is ine less Cloverfield, which is already mentioned.

Krull, I think…

I didn’t even survive very long into Krull…

I just watched Europa One, and I’d say it more or less qualifies as a good bad-ending disaster movie of sorts.