If you take Liara and Wrex in citadel DLC to defeat the clone, their talk in the elevator changes based on Liara having met her father or not. If they never met, Wrex will comment that she has matured, and she will reply that she got used to kill people after the first few hundred victims. If she met her father, she will mention she has just discovered that she´s 1/4 krogan.
If you take James to defeat the clone, the scene with Cortez talking about the damage done to the cargo bay is different.
Edi will malfunction if you take her to defeat the clone. She will also have problems if you take her in admiral korri´s rescue mission.
During the fight against the clone, if you look closely at the cargo bay doors opened, you will be able to see the Shuttle firing at the car with Joker and Steve.
In ME, when you first enter the wards with Kaidan and Ash, there´s one point where you can click in order to trigger a cut-scene. Kaidan will marvel at the size of the Citadel and exclaim "big place." If you take him to the citadel archives in the Citadel dlc he will make the same comment. All the characters have similar observations at this point.
The scientist at the cerberus final base´s videos and the cerberus agent speaking over the comm at grissom academy in me3 seem to have the same voice-actor as admiral korris.
In the blasto movie, when blasto gets his parter´s sister, that´s actually mark meer and jen hale together (the voice talents behind male and female shepard).
You can do the grissom academy rescue mission after priority tuchanka, as long as you refrain from going to the citadel, If you do meet jack, you can tell her that mordin is dead. She will take pity and comment that he used to give some very weird sexual advices.
Edi´s narration on the Synthesis ending will vary in some points based on if you sabotaged the genophage and the resolution of the Geth/Quarian conflict. Also, even if you took Javik on all missions and had him as your most loyal and talked to crew-member, he will never place your name at the board, nor hug Edi.
Even thought characters like Javik, Samantha, Steve and Bakara do have flashback scenes at the ending, and the fact that Mordin can die fulfilling the same role as his and earning a flashback scene, there´s no flashback scene for the Salarian Padok Wiks. As far as i can tell, there´s no flashback for Kelly either.
I could be mistaken, but it seems that Joker´s flashback scene can only be seen on the pre-patched ending.