The title pretty much says it all. What referances would you like to have seen in the Mass Effect trilogy?
Personally I would have liked to see:
If you (femshep) romanced someone is Mass 1, Garrus in Mass 2 but locked in the Mass 1 relationship in Mass 3 without ending it with Garrus. Garrus will referance 'heard it through the grapevine' maybe he can hum a bit of it next time you talk to him in the batteries.
If you had fish in Mass 2 but did not have Kelly save them for Mass 3, when asking after them of someone on the retrofit team (Traynor, Cortez or Adams) they will reference the monty python parrot sketch; 'They are no more, they have ceased to be, they are ex-fish'