Amnesiac Kara goes by the name "Linda," which may be a nod to "Linda Lee Danvers," one of Supergirl's personae from the comics.
This is the first time in which the term "Veritas" is actually spoken when Lilian confronts Lionel about it in one of Lex's flashbacks. The Veritas symbol can also be seen on the shield of one of young Lex's toy soldiers in the same flashback.
In Supergirl (1984), Kara went by the name of Linda Lee on Earth. When Kara Kent is found by Lex in the diner, she tells him that her name is Linda.
At the end of the episode when Clark questions Lex about Kara, you can see the stained glass window behind Lex's desk in the mansion has changed. Up till now it was the Luthor coat of arms, now it's the coat of arms with the Varitas emblem.
Though Lana and Lex would continue to be adversaries into Season 8, this is, peculiarly, the last episode of the series in which Kristen Kreuk and Michael Rosenbaum share a scene together.