If Thane is not imported or you don't speak to him in Huerta Memorial Hospital prior to the Cerberus attack on the Citadel, then during the attack Kirrahe is fatally stabbed while defending the salarian councillor from Kai Leng. However, if Thane is present and dies protecting the councillor, Kirrahe survives and is added as a War Asset.
At the end of the mission on Rannoch, you have a choice to allow Legion to upload the Reaper code or stop it. If it is allowed to upload the code Legion will be destroyed in the process, and if you prevent the upload it will attack and be killed by Tali and Shepard. If Shepard sold Legion to Cerberus during ME2 it will be encountered as an enemy during the raid on Cerberus Headquarters and killed.
At the end of the mission on Horizon, Miranda will die during the confrontation with her father unless her loyalty mission was completed in ME2 and you warn her in advance about Kai Leng via hologram in the Spectre office. Shepard also needs to either use diplomacy on her father or gun him down, as doing neither leads to Miranda shooting her father but being fatally shot by him in the process.
At the end of the mission on Tuchanka, Mordin either dies in an explosion while releasing the genophage cure or, if you choose to sabotage it, Shepard's renegade interrupt action leads you to shoot him, killing him before he can fix it. However, if you have a high enough renegade reputation an additional dialogue option will unlock, allowing you to convince Mordin to delay releasing the cure. This keeps him alive and adds him as a War Asset.
During the final mission on Earth Shepard encounters Morinth, who has now been turned into a Banshee by the Reapers and must be killed.
At the end of the Ardat-Yakshi Monastery side mission Samara will attempt to commit suicide rather than kill her own daughter. However, this can be stopped with a paragon interrupt action. If you save Samara you can speak to her later on the Citadel.