The "social boss battles" in general but especially these:
The first battle against Zeke Sanders, especially given the fact that at this point you (probably) don't have the CASIE aug: you're literally arguing with someone based entirely on your own personal ability to read their actions, body language and personality without any of the assistance like the persuasion bar or the personality summary. Talking down a hostage-taker with no assistance while the hostage is sobbing and crying and the unhinged criminal keeps periodically jabbing his gun into the hostage's head is one of the most intense experiences - and most rewarding when you win.
The battle against David Sarif, where Jensen can make his own boss confess and deeply regret an unknown transgression against the former that ended up contributing to the current mess.
The battle against William Taggart where you confront him about Humanity Front's involvement in the attack on Sarif Industries in the middle of a live televised press conference. This is especially awesome if you managed to convinve Taggart by accusing him of being no better than Sandoval (who has been revealed to help with Sarif attack eariler), which will make Taggart angry enough he starts to curse at Jensen a bit before he can regain his composure.
The final battle against Hugh Darrow, where Jensen can win a debate about the future of mankind against a billionaire Nobel Prize winner.
Made into an even bigger Crowning Moment of Awesome if you have the CASIE. Jensen, using his enhanced intuition, realises that Darrow is genetically imcompatible with the augmentation technology he invented and despises the world because of it. He then proceeds to mock the old man with it until he breaks down.
Don't even try to deny the feeling of elation and satisfaction when you hear these four words: "Any time, fly girl."
Especially if you managed it on a pacifist run. On hard.
There's a very fun and satisfying way to beat the final stage, as there are many unarmed zombie-like enemies- just make sure to stock yourself up with battery replenishing candies and jars from LIMB clinics and buy the reflex aug that lets you perform double takedowns.
Alternatively, if you've been carrying the PEPS this far through the game, you now have an incredibly effective, efficient, and satisfying method of non-lethal crowd control at your disposal.
Heck, even Eliza seems to agree that with this ending. The other three endings have her say "So be it, then" in a resigned tone. The above ending? "We have little time left, Adam. And might I say, it has been a pleasure..."
Somewhat undercut by the fact that the rest of the Illuminati are still out there. Oh, and the station you're destroying has hundreds of innocent people in it.
Listening to some of the NPC chatter in The Missing Link makes it clear just how much of a badass Jensen is. One NPC will even point out that half the base is scared of Jensen, especially if he's been running around killing everyone.
Even if you're doing a total stealth Pacifist Run, they're still terrified of him. After all, there's a guy loose in the complex who's a heavily augmented Super Soldier and who managed to take out five heavily armed and well-trained soldiers in a greatly confined space, while disoriented and surrounded after being forcibly woken from stasis, before finally going down — and it still took eight men to do it. And even though they can tell where's he's been, no one knows where heis. As one guy says, "Do not let the low casualty count fool you. It only means he is more resourceful and more dangerous."
Getting through the first level by knocking out every single Purity First man without any of them ever suspecting a thing. Even the otherwise unpleasable SWAT are damn impressed and actually acknowledge that sending you in first was probably a good idea.
Using the Typhoon can be one. There's nothing quite like ending a boss battle in the first second or wiping out a giant robot the moment it deploys.