For simplicity's sake, I'm not going to keep repeating "If X survived ME2", because that'd just get annoying.
-Recruiting Javik is optional. He'll never be mentioned if you don't, and it's safe to say Cerberus didn't keep him around for long.
-If Grunt's loyalty mission wasn't completed, he won't survive his stand against the rachni. Well, his loyalty power was Fortification..... (If he died, was never awakened, or wasn't accepted into Clan Urdnot in 2, his replacement, Urdnot Dagg, simply dies.)
-If Kasumi wasn't loyal, after the console explodes in her face, she disappears. It's ambiguous if she actually dies or just slips away because she doesn't trust Shepard (the writers seem to lean towards the latter), but either way, she's outta here.
-If you leave the Grissom Academy mission for too long and it disappears, Jack will end up captured by Cerberus. She'll be reconditioned into a Phantom and fought as a mook in the Cerberus Base mission, identical to the other Phantoms except that she still uses her voiced lines from 2. (If she died in 2, one of her students replaces her during the mission and dies near the end. If you skipped the mission without her, it never comes up again.)
-If Maelon's data was destroyed during Mordin's loyalty mission (which results in Eve's death), and if Wrex is dead, Mordin can be convinced that the galaxy can't handle a krogan resurgence and will sabotage the genophage cure, then join the Crucible project as a war asset. Otherwise, either he'll die deploying the cure, or will be shot in the back by Shepard and die inches from releasing the cure. (If Mordin is already dead, his replacement, Padok Wikks, has the same options, but he just goes into hiding instead of becoming a war asset.)
-If you sabotage the genophage cure while Wrex is alive, he finds out. He'll eventually ambush Shepard on the Citadel, essentially committing suicide by cop. (His replacement, Urdnot Wreav, never finds out.)
-During the Cerberus coup, if you haven't bothered to try to mend fences with the Virmire Survivor, they'll refuse to stand down and have to be killed by either Shepard or another squad mate. If you started to mend fences but didn't do enough, or if you did but refuse their request to rejoin the Normandy, they'll join Hackett's fleet instead as a war assett and are never seen again.
-Also during the coup, Thane will fend off Kai Leng from assassinating the salarian Councilor, but takes a fatal wound in the process and dies shortly afterwards. (If he's dead or was never recruited, Captain Kirrahe takes his place. If both are dead, the Councilor dies.)
-At the end of the Ardat-Yakshi monastery mission, Samara will kill herself unless stopped with an interrupt.
-At the end of Rannoch, Legion will die, either uploading himself to grant the geth true sentience, or being killed by Tali (or Admiral Raan, if Tali's not present) to stop him from doing so. Notably, this is the only time in the entire trilogy that Tali will actually use that knife strapped to her boot.
-If you fail to make peace between the geth and quarians, and side with the geth, Tali will walk off a cliff in despair. To twist the knife further, the game gives you a Paragon prompt to try to save her, but it doesn't work. (If Raan is present instead, she shoots herself in the temple.)
-If Zaeed wasn't loyal, he dies saving Din Korlack from Cerberus bounty hunters.
-If you don't keep Miranda up to date when she asks throughout the game (granting Alliance resources, warning her about Kai Leng, etc), she'll be fatally wounded by Kai Leng and bleeds out shortly after killing her father. If you romanced her in 2 but switched to someone else in 3, she dies regardless.
-Nyreen dies taking out a pack of Adjutants near the end of Omega.
-If Javik views the memory shard, he decides to find the graves of his old crew and then kill himself after the war is over.
-During the final mission on Earth, if Morinth was recruited in 2, she appears as an extra Banshee and has to be killed.
-If you blew off Cortez throughout the game and never helped him get over his grief, he dies when his shuttle crashes after dropping you off.
-If your war assetts are too low, during the Conduit run, your squadmates will be killed by Harbinger's beam. Notably, this is the only way (short of picking Refusal) to kill Liara or Vega.
-While it takes longer than the other two early-mission sacrificial characters, Anderson succumbs to his wounds and dies after the final confrontation with the Illusive Man.
-And finally, the endings:
Destroy: EDI dies. Shepard will also die unless you've collected enough war assetts.
Control and Synthesis: Shepard dies.
Refusal: The entire galaxy is slaughtered.