In Mass Effect 2, during Garrus' loyalty mission, if you never met with Harkin before, or has a Not Imported Save from ME, he will take a few seconds to recognize Shepard, and if you Imported a Save where you met him, he'll recognize Shepard straight away.
In the Mass Effect 3 Select a Squad Screen, Javik is seen with a Disciple, but in-game he isn't trained with Shotguns.
* Also, his biotics are blue, instead of the Green ones seen on the Flashback on Eden Prime... The only one is his exclusive power, Dark Channel.
# Even if you didn't activate and/or sold Legion to Cerberus, Javik will still refer to the Geth VI as the "Legion Machine"
In Mass Effect 3 Background Screen, while loading the game and before opening the Terminals, you can see Shepard (I think it's Female Shepard) with Cerberus Colors.
In Mass Effect, The C-Sec Officer that Jahleed is talking to is the same that was telling Wrex to stay away, when meeting them in the C-Sec Academy.
Mass Effect Galaxy was originally named Jacob's Story
Dr Cayce from Firewalker Pack was originally meant to be the crazy scientist Manuel from Eden Prime. In one of the cut dialogue he even mention Shepard and the punch that s/he gave him. (PS: I think it's still is, but since is Cut Content, it could be another crazy Scientist) (Source: https://www.youtube....D98C5B2F05#t=93 - From all the way to the end...) TIME: 1:33 till the end of video
Barla Von was meant to be dead in Mass Effect 2 events, according to a News Report. However, it also got cut. (Source: https://www.youtube....98C5B2F05#t=153) TIME: 2:35
When using her powers, Jack will yell "I will destroy you!" Making a reference to Mass Effect(1) enemies.
Martin Sheen sucks a pen to simulate smoking. (Source: https://www.youtube....SFMZ1nWVv8#t=25 ) TIME: 0:25 (It seems this one skips to the right time... The others don't. What a bummer
)
Edit: For some reasons, it isn't going to the exact moment of the video... So, I'll leave the timer.