Death of Green Arrow - Shocking they decide to kill Oliver in Supergirl when it probably should've happened on Arrow. But whatever.
Superman vs Superman - My vote. Seeing old vs new was great to see. Personally, I was rooting for the old!
Infinite Earths are Gone - Not sure how I felt about this to be honest, other than it being a Infinity War type cliffhanger with two parts left.
Fight at the Dawn of Time - Not the best fight, sure, but it was cool seeing Mobius vs Oliver: "You have failed this universe!"
The Justice League is Born - Kinda exciting, kinda underwhelming. Proabably because Oliver was gone. Though it did bring back memories seeing the name "Gleek" and hearing the old Super Friends theme music.
Of course, one has to mention Bat stuff, like Kevin Conroy's entrance in Part 2; his voice is heard first before Bruce himself is seen with Danny Elfman's theme playing. Granted, that theme played on Part 1 on Earth-89 but still, to see the man DC fans have known as THE Batman...Perfection! Just my opinion.