During the intro sequence for the mission where you are about to land on Rannoch, Commander Shepard is standing in the Normandy's bridge speaking to Joker about the tons of enemies. Joker laughs it off and says that with the Normandy's stealth drive engaged, the only way for the Geth to notice you is if you all start singing the Russian national anthem, a direct reference to the 1990 film.
At the start of the game while fleeing Earth, you can see the child you will eventually speak to running away from Husks. Before the part where you see Husks climbing up the wall (the first time you shoot at something), you can see the boy looking below, looking over the railing. When the Husks arrive and Anderson coaxes you to shoot them, watch the boy run into the building and lock the door. The building is blown up seconds later, but he apparently survives in the vent.
During the part where you're on planet Gellix rescuing the defected CERBERUS scientists, just after the scene where you talk to Jacob about things and right before you speak to Dr. Brynn, there is one ex-cerberus official (Dr. Brown) mourning to her husband right beside the screen (you can`t miss it). Speak with her and you`ll automatically receive a +2 reputation. After that, pause the game and then save your data. Load it once again and you will notice that you`ll be in the same moment before you saved, and Dr. Brown is in the exact same position. Speak to her again and gain another +2 reputation. Do this as much as you want until you fill your reputation meter.