Supergirl says to Flash, "this is becoming an annual thing," referencing the crossover events from the previous two seasons.
When Barry and Oliver are looking for Cisco, Barry references Flashpoint (2016), when he rewrote reality and Cisco wasn't much help.
In DC comics, the "Book of Destiny" is also known as "Book of Souls", and belongs to Destiny of the Endless.
A woman says "bizarro" when she sees Superman fighting John Deegan/Superman, a reference to Superman's exact opposite personality clone from the comics, Bizarro acting is similar to opposite Meaning day "No" means "Yes," "up" is "down" and so on.
This episode introduced us to Earth One doppelgänger versions of James Olsen and Alex Danvers.