Yeah, all of the shows were altered, except for Batwoman (which was too new).
We know Marsdin was still president, which means that Earth-Prime, like Earth-38, probably had a one-term Obama. In Earth-1 and the real world, he lasted two terms. The shows introduced a different character in Invasion, instead of having Trump like in real life, but post-Crisis, she's been replaced by someone new.
Regarding villains, we know that any Flash episode involving multiversal characters played out differently. That impacts on Harrison Wells in particular, but also Gypsy, Breacher, and Jesse Quick.
Same goes for Black Siren in Arrow, who is now an anomaly, a remnant of a world that never existed. Most of Arrow played out differently due to Tommy Merlyn and Moira Queen never dying. Season 7 was particularly affected, as Emiko Adachi was not only resurrected after the Crisis, she was also never a villain. As such, that season would effectively have ended with the death of Ricardo Diaz and Oliver's release from jail.
Legends of Tomorrow loses the episode Star City 2040, which Crisis retconned to being an AU that was erased instead of a bad future (a necessary change as it's contradicted by the new Green Arrow and the Canaries future) and the episodes involving Leo Snart of Earth-X would've played out differently since he now never existed.
As for Supergirl, Lex having good publicity and owning the DEO changes a lot. Lena never rebranded Luthorcorp to L-Corp, so her introduction would've been different. Kara would've never received the breaching device at the end of Invasion, because she was on the same Earth as Barry already.