Tokyo Babel
Tokyo Necro
Bradyon Veda
Komorebi no Nostalgica (It is after a massive world war between sentient humanoid AIs and humanity that concluded with humanity's defeat and a peace agreement. Things have settled in the wake and society has been rebuilt, but problems remain. It is primarily a nakige.) Edit: To clarify, this is not a 'wasteland' style post-apocalypse. Rather, what was lost was history and culture, as a major hack destroyed the internet archives which had become responsible for retaining most of human culture and history from the late nineteenth through the twenty-first century.
Sousei Kitan Aerial (Muv-luv alternative type situation)
Hotel
Venus Blood Hypno/Hollow
Shuumatsu Shoujo Gensou Alicematic
Any and all of the Soleil games by Skyfish
Baldr Sky
Fake Azure Arcology and Re:Birth Colony (games based long after a massive apocalypse, both based in arcologies)
Owaru Sekai to Birthday
Reminiscence (centuries post-apocalypse, underground arcology)
Sorceress Alive
Strawberry Feels
Harumade, Kururu
Natsukumo Yururu