The Illusive Man was first intended to turn into a Reaper creature in Mass Effect 3. This plan was later scrapped as the developers wanted to give players the satisfaction of fighting a character they knew rather than a random creature, highlighting the fact that the Illusive Man's weapon is his intelligence, not his physical strength.

The pilot, Joker, references the film The Hunt For Red October by saying, "The only way they'll notice us is if everyone starts singing the Russian national anthem."

After the "Shut down the Geth server" mission, you can go check on Ashley. She will be on the floor, hungover.

If Wreav is the Urdnot leader during the mission Priority: Tuchanka, he will urge Shepard to "fight like a Krogan". This is a reference to the chorus of the Mass Effect fan song 'Commander Shepard'.

If you chose Kaidan Alenko as the living squad member (leaving Ashley Williams to die in Mass Effect 1) you can see Ashley's ghost on the Citadel in a cutscene. If you chose Ashley in Mass Effect 1, nobody is standing in her place.