In ME3 Citadel "Agent Brooks" will have at least 2 different things to say about the Illusive man when she reveals her true agenda. If you do it very early she will say that they had different methods. If it´s done later in the game, she will say that he has become indoctrinated.
In the same scene, when shepard and his squad become trapped inside the field he or she will really fire the weapon being equipped at the moment. Some of the guns can make amusing effects during the scene.
Again, in the same scene, she will mention of cerberus asking aliens for help. If Garrus or Tali are brought along they will trade a few comments.
In ME3 leviathan, while in the doctor´s office you can inspect a piece of sovereign. If you did play ME1, shepard will make a sarcastic comment about "the vanguard of our destruction. How is that working out big guy???". If you did not (I was using a ME2 save) he/she will simply say that it better be shielded.
During the trilogy in some places the game will recognize that your character is a biotic (or at least has biotic influences, even though bonus powers do not count). Kaidan will have different lines in ME1 while talking to you on the ship. Also, if you bring him along to the asari monastery he can also add a remark.
The scene in ME3 with Liara in your cabin will also differ. It always differs based on your renegade/paragon score, origin and service, but also your class.
If there´s a dispute in the dlc citadel during the party with liara and james (and possibly other guests as well) arguing about biotics, whether your shepard is a biotic or not will play a role during the discussion.
In ME3 Omega, if you convinced Mordin to remain alive incognito (wreav needs to be the ruler, with Eve being dead because mordin´s loyalty mission was never done or his assistant´s work was intentionally erased), Shepard will not lie to Aria when they enter the gozu district by saying that mordin died. He will simply remain silent.
Yesterday I saw something really cool for the first time. In the citadel dlc jack will make an appointment with you you at the virtual arena. Ok, so far so good. But the end of the scene is quite different if you´re romancing her. And there´s also a variation if you´re using a biotic (and possibly - I believe - a biotic derivate class). I had a save on PC just prior to meeting Jack so I hacked it with the gibbed editor and altered my profile to soldier class to see the differences in the dialogues and attacks. They are both barricaded against a boss cerberus heavy mech. If you are using soldier, shepard will provide cover for jack with his gun. If you´re a biotic, both will start triggering lots of biotic explosions.
Now I´m curious to see if drunk tali will mention eezo during the party since when a romanced jack visits shepard she never brings eezo (her pet varren) along. At least it´s not showed.
Man... So many years later... So many plays after... And one can still find new things in these games. The amount of conditional content is shocking. I don´t think the creators will ever receive enough praise for the work they did, since most people will simply have one or two plays, most of them aiming at a perfect score with most people alive (all alive in me2). You know, trying to find the so-called "best way", without realizing that all possible scenarios are legitimate and each one has its own complexity. Which is why I never dared to complain about the (entirely optional) DLCs being sold at high prices. Very few games could entertain me for hundreds and hundreds of hours years after I purchased them. And most of the ones that did such a feat usually required a second player or even a whole team or community to keep the activity interesting. I just hope ME4 does not ruin the ME experience.