When Supergirl says to Overgirl "General, would you care to step outside?", it is a reference to Superman II (1980) when Superman says the same thing to Zod.
Earth-X's Snart makes an overture towards Sara, a callback to their implied relationship in Season 1, thereby also suggesting that he, like Sara, is bisexual.
Former Arrow actress Susanna Thompson (Moira Queen) has an uncredited role as the voice of the the A.I. of the Wellenreiter.
Other than a couple of cameos, Russell Tovey is technically the only real guest star in the entire crossover. The remaining cast members have regular or recurring roles in one of the Arrowverse shows.