In ME2 After recruiting Garrus and;/or Mordin, take him/them back to Omega soon and Edi will read a piece of news regarding their backgrounds. Depending on how you deal with mordin´s assistent (saving him or not) will impact the news. Similar scenes can happen featuring thane and garrus on the citadel after their missions when you go to the port, and grunt/mordin in Tuchanka. Samara will also have a special scene if you have her with you on illium and talk to the asari that previously was concerned about a inter-species incident (close to the taxi port).
In ME2, the conrad verner mission can have two paragons and two possible persuade renegade conclusions if you trick the asari. They all depend on picking or not the middle option with conrad as soon as the asari gets arrested.
I took Grunt and Mordin to the Krogan home-world to do their missions. Spoke with wrex, but not the shaman, did Mordin´s mission, but dit not take grunt with me. Then tried talking to the shaman without having grunt with me and Uvenk was there talking to the shaman about grunt.
In ME1, if you use the neutron purge in noveria to kill the rachni prior than meeting the queen, the conversion with her will be different in some points than if you haven´t done it yet.
You do not need to take samara with you to omega in order to do her loyalty mission. The design of the citadel council chambers that appears on the map in me1 is identical to a reaper design.