In the penultimate episode of season seven, Mark treats a boy with signs of parental abuse. The father comes in, insisting that he wasn't abused, the boy finally admits the abuse and DCFS put him in protective custody. In the season finale, the father snaps and goes on a rampage, shooting up anyone and everyone who gets in his way as well as the people who helped get his son some medical treatment. He killed at least nine people, including the neighbour who brought in the son, and injured at least twelve, including Adele Newman (the social worker who often worked with the staff, especially Doug Ross). Mark suspects that he might try to go after Elizabeth and their baby. Finally, the father gets shot by one of his victims and is taken to County where the ER doctors work to stabilise him. The father keeps screaming for his son and threatening to kill anyone who helped take him away. He sees Greene and starts threatening him as well. Greene finds out that the shooter would have gone to his house if he hadn't been shot. They stabilise him and take him up to the OR. Greene finds himself alone with the shooter when the elevator doors unexpectedly close. The shooter starts coding and Greene prepares to defibrilate. He looks in the shooter's eyes and instead decides to let him die, shocking the air so that the monitor will show he attempted to save him. The shooter looks in Greene's eyes before he dies.
"Bob", a Polish immigrant who for most of her appearances in Season 1 worked as a clerk in the ER, performing an emergency procedure on a patient and saving his life. It turns out that in her home country she was a cardiothoracic surgeon and was studying for her board exams while doing scut work at County.
This later leads to a minor CMoH when Carter finds her in tears, thinking she's ruined her chances of ever getting certified in the US. Carter reassures her, offers to help her with her English for the board exams, and escorts her back into the reception area, where "Dr. Bob" is greeted with applause and cheers by the rest of the staff.
Peter Benton doing that ruptured abdominal aneurysm in the Pilot, despite the fact that he was just a resident, had practically no idea what he was doing and had (to start with) almost no one to help him do it.
Peter Benton doing procedures on a patient strapped to a load of dynamite. They trigger a detonator and everyone else clears the room before it blows. Peter just takes the detonator and throws it before ducking down, surviving unscathed.
Peter Benton staring down an abusive Cop husband whose wife came in for treatment after suffering his abuse. He says to him 'What do you think when you're beating her? What a big man you are?'
Then the very nice follow up later in the episode when said cop is brought into the ER. The other cops (one of whom Benton tipped off to the fact that the guy was beating his wife) claim that the guy fell down some stairs while chasing a suspect, but it's pretty obvious that they took him somewhere and beat the crap out of him.
Peter Benton punching a prick orthopedic equipment salesman who parked in his spot. The guy challenged him to do something about it, so Peter threw his case of equipment out. The guy then tried to take a swing at him with a prosthetic leg, so Peter ducked and then punched him in the face.
Peter Benton beat the crap out of Malucci, who really needed to be taken down a peg, for referring to his nephew as a banger.
On Peter's last day at County he manages to save a six-year old boy who was accidentally shot by his mother. Romano claimed the boy was a goner. Peter told him to either shut up and help or get out.
Doug Ross' rescue of a boy trapped in a flooding storm drain, under increasingly difficult circumstances. The shot of him triumphantly emerging from the river after getting the boy out is one of the most memorable in the show's decade-and-a-half run.
Carter taking charge after the hospital is contaminated by benzene and Weaver is incapacitated by the fumes. He takes an impossible situation and does the best he can with it, resulting in a lot of lives saved and him earning a personal commendation by the leader of the hazard team, even as the latter is calling out the whole situation as a complete mess that should never have happened.
Gabe Lawrence saving one more life as he leaves the hospital after recognizing his encroaching Alzheimer's Disease.
Corday's final confrontation with the serial killer who'd been psychologically tormenting her for weeks, coming up with the one way to beat him as she declares the very reason why she's unambiguously better than him, and she'll never be seeing him again. Then she turns and walks out, leaving him to impotently shout for her to come back.
Corday was treating a patient whose leg and voice she'd saved earlier. The patient was coding and Corday and Romano tried to revive her. Romano was ready to give up but Elizabeth just wouldn't accept that a patient she'd worked so hard on would just die. Romano tells her its over. Corday tells him to stop being such a prick and eventually revives her.
"You wanna fight? We'll fight, but one way or another, you're getting your ass in that van."
Weaver and Gallant performing an emergency C-section in an ambulance surrounded by rogue electrical wires, saving both mother and baby.
In an early Season 7 episode, Abby (as a nurse) assists with the delivery of a micro-preemie who does not survive. When she returns with the husband to find a doctor with a group of med students "showing off" the baby, Abby then proceeds to rip into him about giving the father false hope and then puts him in his place regarding how to show compassion to the family. The doctor is left speechless.
Kovac actually killed a mugger. Even better, he managed to recover quickly and beat him up mercilessly after said mugger blind-sided him. Unfortunately Kovac then felt rather guilty about the whole incident.
Kovac beating the crap out of Abby's abusive neighbor, after he breaks her nose for convincing his wife to leave him.
Weaver has fired incompetent resident Dave Malucci. Ostensibly for having sex with a paramedic while on duty, but mostly to ensure that he takes the blame for the death of a patient (conveniently ignoring her own failure to supervise him). After all of Dave's pleas leave Weaver completely unmoved,he proceeds to deliver an epic"The Reason You Suck" Speech. Starting with calling her a "sad, cold-hearted bitch", telling her that "nobody here likes you", and capping it off by declaring that she has nothing in her life aside from her job. It's marred by his unfortunate use of a homophobic slur at the very end, but other than that it was thrilling to see Weaver finally get a dose of the public humiliation she had so frequently doled out to the staff for 6 years. On the other hand, to viewers more sympathetic to Weaver, watching her stoically take every bit of petty, unprofessional abuse Malucci could dish out and still tossing his mediocre ass out on the street was pretty damn satisfying.
Jeanie Boulet voluntarily outing herself to her co-workers as HIV-positive not for their sympathy but so that they will stop talking about her in the hypothetical.
One could argue that Archie's development into a seriously competetent professional qualifies. When Carter tells him to "set the tone" as he departs in Season 11 (similar to how Greene told him to do so), Morris is confused by the sentiment, leading Carter to shake his head and reply, "Never mind", as if to retract on his passing the torch, demonstrating the immaturity of Archie's character at this point. However, after getting taken hostage in Season 14 and seeing his taker (who he had bonded with over the course of the episode) get shot dead by a sniper, Morris makes an attempt to ground himself in reality. The further death of his best friend, Greg Pratt, further forces him to confront life's harsh realities, and by the end, he's become one of the most competent doctors in the ER (and maintained a steady relationship with his police officer girlfriend). When Carter makes is return in Season 15, he's quick to notice the shift in personality:
Carter: Looks like you followed my advice, Morris.
Abby: If I were in trouble, Archie, I would call for you. I would. I would trust you with anything. (Beat) And I didn't always feel that way, but I do now.
Mark is treating a patient who has revoked her DNR order. Weaver, of course, objects and tries to take control of the situation. First by suggesting that Mark's in no condition to handle the case because of his mother's recent death, then by threatening to take over the patient's care, and finally by nagging him endlessly as he tries to revive the woman. A fed-up Mark finally grows a pair and yells at her "SHUT UP, Kerry or GET OUT!" And she promptly shuts up.
Doctor Benton is filling in at a small backwater hospital in the Deep South, and spends the episode gradually adjusting to his new environment, and gaining the trust of some of the racist locals. When it's time for him to go home, there is an explosion at a dock, and he ends up performing some very expedited emergency medicine on a badly injured man, assisted by one of the aforementioned racist locals. This emergency work included using a large roll of saran wrap as a bandage due to the large gash in the patient's midsection.
Doug punching out an abusive parent after discovering that his boot matched the shoe print he found on his daughter's back.
Admissions clerk Randi punching out a patient who pulled the fire alarm because he was angry that the doctors wouldn't take his migraine headache ahead of the massive trauma they were dealing with.
Weaver: Stay down. You move, and I'll let her at you.
All of the original cast members as well as some of the secondary/tertiary ones who joined in seasons 2-4 not only returning for the final season, but stepping back into character as though it had been merely days instead of years that they had played the role.
The last few minutes of the series finale. Specifically, the staff evaluating the victims of an industrial accident, combined with the full theme music, and the pullback shot of the hospital exterior. It was really a shining example of what ER did best.
Any of the long, frantic "runner" scenes are a CMOA for the cast and crew.