"This is what I was made for, isn't it? This is why I exist? Alright. Let's do this!" — the Helios ending
Tracer Tong's ending, with the enthusiasm in his voice, uplifting music, and a quote from Khalil Gibran: "Yesterday we obeyed kings and bent our necks before emperors. But today we kneel only to truth..."
JC Denton escapes from Bad Guy HQ and still spares the time to tell The Dragon what a corrupt asshole he is. Badass, party of one, your table is ready.
JC Denton: Well, since that makes you my new boss, take a good look at Manderley's dead body. Consider that my resignation. I don't have time to write a letter.
Also, after managing to avert an enemy atomic strike by capturing the silo just before its ICBM launches, does Denton chalk up this victory and call it a day? Hell no. Denton retargets the missile himself to wipe the Big Bad's surface defenses off the map, has his chopper pilot drop him off right at ground zero, and enters the Big Bad's underground lair through the nuked wreckage!
When you get to Area 51, if you ran from Walton Simons rather than confronting him at the Ocean Lab, he'll be there to greet you. JC's response is one of the coolest things ever.
Walton Simons: You take another step forward and here I am again, like your own reflection in a hall of mirrors.
JC Denton: That makes me one ugly son of a bitch.
Bob Page's entire raving speech in the intro is amazing, and perfectly complimented by the music.
...or better than kings. (music goes quiet) GODS.
And JC's reaction to Page's insane hubris is just as amazing.
Bob Page: Soon, I will become pure energy. I will burn like the brightest star.
JC Denton: You're gonna burn, all right.
The killphrases for Anna Navarre and Gunther Hermann, or rather, how JC uses them.
Consider this: MJ-12, and their predecessors, the Illuminati, have been scheming for years, decades, perhaps centuries if Everett and Lucius DeBeers are to be believed. The conspirators have been accumulating power by subverting the academic, political and financial institutions of the world their entire lives. JC Denton starts as a rookie special agent on the pier of Liberty Island, with nothing but a pistol and an electric prod to his name. The only real advantage he has over a normal person is the modular nano-augmentation system he was literally built from the ground up to test - something that also allows the conspirators to both spy on him at any time and kill him within 24 hours at will. Within a couple of weeks, he's completely disassembled the entire worldwide conspiracy and brought its kingpin to the point of begging for his life. Badass, thy name is JC Denton.