The fight between Superman and Doomsday. Superman's last attack against Doomsday one-ups the final blow in the comic book version of the story. Beaten and spitting blood, Superman musters up enough strength to grab Doomsday, fly him clear up into the stratosphere before taking him into a death plunge whaling on him the whole way down. Doomsday dies, Superman actually lives long enough to get back on his feet, climb out of the crater and ask if everyone is okay before dying.
It may not be a hero's choice, but one can't help but feel a certain amount of grim satisfaction when Clone!Superman threw Toyman down to the asphalt from a hundred feet in the air after hearing the news about his recent murder of a 4-year old girl.
A similar instance when he confronts Luthor is pretty satisfying too, especially after you've seen Luthor brutally beating him in his "rumpus room". Luthor tries to goad him into entering the room for a second beatdown. What does Clone!Supes do? Lock the door, and rip the room out of the building before throwing the whole thing straight through it.
The line he gives before this act is the icing on the cake:
Lois Lane, period. The Badass DamselIntrepid Reporter, who, even when Superman is not there to save her, is always in the thick of the action, doing the right thing. She rescues Toyman's children hostages, gets an upper hand on Lex Luthor and uncovers his plan, and when Real!Superman is fighting his clone, and all hell is breaking loose, she comandeers a military jeep, goes around the city looking for the Kryptonite gun, finds it and then shoots the clone with it, ensuring Real!Superman's victory.