Fridge Brilliance: Christina being unable to deal with Burke being shot makes a lot more sense after we learn that her father died in a car accident right in front of her when she nine. However, she manages to overcome this, and fares much better when Owen is shot.
Episode "If/Then" (the alternate universe episode) has a lot of them.
Charlie who had be previously shot says at one point "Shoot me!"
Bailey in braids: a call back to an earlier episode where she was shown as a meek intern known as Mandy wearing cornrow braids.
Why would Kepner and Mer be friends? Mer hates her... oh, wait, Mer hates her because Kepner had a crush on Mer's husband, Derek in the real world. In this alternate universe Mer and Derek never got together, so Mer never hated Kepner for having a crush on her husband.
The "I'm just a girl in a bar" dialogue between Meredith and Derek is the same conversation they had in their first meeting.
The music has been used in previous episodes. "You Wouldn't Like Me If You Met Me" by Tegan and Sara was used in S1 E2; "Fools in Love" by Inara George was used in S2 E3; "Into the Fire" by Thirteen Senses was used in S1 E1; "Portions for Foxes" by Rilo Kiley was used in S1 E1; "Ruby Blue" by Roisin Murphy was used in S2 E3.
Karev says "I always say never mess with the crazy chicks," which is ironic because he was involved with Rebecca who went crazy and had to be committed and right after, he says "she's probably gonna go full-on Izzy," referring to the only other serious relationship he ever had on the show.
Cristina and Meredith have the "We don't have to do the thing where..." dialogue previously used in a few episodes, originating in S1 E1.
Fridge Horror: "You have apple hair. I threw a pancake in the river! The River!" It seems funny at first. Until it's not.