Towards the end, we have Yukari emptying s gun in a wall of mirrors, much like Baby-Doll did in that BTAS Episode.
A subtle one is from when the When the Wind Blows where Yuuka is panicking about a deathly white hand, much like how Hilda was panicking about a rat.
To When the Wind Blows and the film gets a passing reference in Chapter 6, when Yukari suggests on building an inner core or refuge. Similarly, Ran, like Hilda, did point out that there really isn't enough room for more than two.
Another one would be Sakuya holding out for emergency services.
Another one would be a shoutout to This Is the End where Seija eats half of their rationed food and used some of their rationed water to bathe.
Also what Yuyuko says about her in her narration
Yuyuko: The little fucker's gained weight.
Also, again to The Triplets of Belleville, when Ran responds to an absent Yukari's voice, like Champion responded to an absent Madame Souza's voice.
Chapter 109 features a shoutout to Dante's Inferno, which ties in well, if you consider that chapter features a widowed Ran thinking about the happier times with her passed on husband Ren and how much it makes dealing with grief worse
Some of Ran and Yukari's diary entries are shoutouts to the live action adaption of Animal Farm and the character Jessie (who's narrating parts of the movie), which was playing the background, as Amoridere was writing.
Yuuka's is even more of shoutout, in that she would sound almost identical.