Despite his reputation as the grim-faced, stony-hearted Dark Knight, Batman's character has a fundamental compassion; what drives him more than anything is ensuring no-one suffers the same pain or loss he did, and his rule against killing is fueled by a belief in redemption.
There are times while facing one of his adversaries, Batman put aside his usual tools of fear and violence in favor of empathy.
10 Justice Lord Batman
The Justice League of a parallel universe, the Justice Lords, seized control of their world after a power-mad Lex Luthor was elected US President - discovering the reality of the DCAU Justice League, the Lords abducted their counterparts and traveled to their world to bring the same order they had to their own. When confronting his doppelganger in said double's Batcave, the League Batman chastised the Justice Lords for seizing power.
Unfortunately, the Lord Batman knew exactly the right thing to pierce League Batman's argument and soul in one blow - "And with that power, we've made a world where no eight-year-old boy will ever lose his parents because of some punk with a gun!" Stunned, the League Batman drops his weapons and resignedly declares "You win." However, it's not long before the League Batman turns the tables by asking the Lord Batman if their parents would be proud of the totalitarian world the Lords have built.
9 Poison Ivy
As an eco-terrorist, Poison Ivy has more noble goals than most of Gotham City's other evildoers, though Batman still can't overlook her murderous extremism. However, the Dark Knight has still shown sympathy for Pamela Isley on occasion, from Batman: The Animated Series episode "House & Garden." Isley seems to be rehabilitated, and that's something Batman wants to desperately believe. Unfortunately, her domestic ruse comes undone in the most horrifying and sorrowful way possible.
8 Clayface
The Matt Hagen of the DCAU didn't choose to become Clayface, so when the actor-turned-shapeshifter resurfaces, in poor health, during "Mudslide," Batman pleads with Hagen to work with him so they can cure his condition together.
Unfortunately, Hagen isn't interested in removing his abilities, but augmenting them; knowing his capacity for criminality, Batman refuses to let Hagen receive a treatment that would've stabilized his powers and removed his default "Clayface" form.
7 Harley Quinn
Batman's usually felt a taste of pity for the erstwhile Dr. Harleen Quinzel, not so much due to her actions but for how she was psychologically broken down and remade by the Joker into his hopelessly devoted moll.
In the B:TAS episode "Harley's Holiday," when Harley is judged sane and released from Arkham, Batman is genuinely proud of her, even if his stern demeanor hides it. Unfortunately, on Harley's first day of freedom, a misunderstanding at a clothing store puts her on the run again. Still, in the episode's last scene, when Batman escorts her back to Arkham, he gifts her the dress she'd been attempting to purchase as a sign he still believes in her rehabilitation, earning him gratitude (and a kiss) from Harley.
6 Baby Doll
B:TAS occasionally created original villains, one of whom was Baby Doll, in truth actress Mary Dahl, whose affliction with "systemic hypoplasia" kept her from physically-aging past the age of five. Dahl quit her sitcom "Baby Doll," then utterly face-planted into a move into more serious acting. So, in her eponymous debut Batman episode, she begins kidnapping her co-stars to recreate the one time in her life she felt accepted.
The episode easily has the makings of a farce, but the closing moments are surprisingly touching; after Batman pursues Dahl into a carnival, the pair stumble on a house of mirrors. There, one of the distorted mirrors creates a reflection of what Dahl would look like if she'd aged properly. Dahl breaks down in tears at the illusion and clasps Batman's leg; instead of carting her away the Dark Knight stands solemnly still, letting Dahl's emotions run their course while offering a consoling hand atop her head.
5 Mr. Freeze
Batman has seen plenty of great evil over his vigilante career, so in "Heart Of Ice," when even he exclaims "My God!" with equal measures horror and sorrow upon witnessing a recording of how Victor Fries had his life destroyed, it's clear the event was soul-crushing.
Though Batman never lets Freeze go through with the vengeful murders, the icy villain is one whom Batman has shown consistent empathy for, often appealing to Freeze's humanity when he faces him, all the while hoping Freeze can cure his own condition and that of his wife Nora's.
4 Two-Face
Many Batman stories depicted District Attorney Harvey Dent as both an ally of Batman and acquaintance, sometimes even friend of Bruce Wayne, so Dent's transformation into Two-Face was a sting which still pains the Dark Knight. The two foes' greatest moment of shared humanity comes at the end of The Dark Knight Returns' Chapter 1: Bruce Wayne funds surgery to repair Dent's face, but after being released from Arkham, Harvey (sporting bandages around his face) returns to his life of crime around the same time Bruce puts on the cowl again.
Batman initially believed that Harvey had scarred himself once more, but after ripping the bandages off, he sees that isn't the case - the surgery simply couldn't fix the far deeper scars in Harvey's psyche. Having rustled with his own inner demons and failed to fight them off throughout the chapter, Bruce finally sees himself and Harvey as the mirror of each other they are.
3 Red Hood
Batman's failure to save Jason Todd, the 2nd Robin, from being tortured then murdered by the Joker remains his greatest failure, one he spent years agonizing over. So, in Under The Red Hood, when Jason resurfaced as murderous vigilante Red Hood, it makes that Bruce's first priority wasn't apprehending him, but in trying to talk him down.
Sadly, despite his attempts at apology and desire for reconciliation with his surrogate son, Batman can't bring himself to do what Jason wants most of him - kill the Joker - and so the former Dynamic Duo maintain a frosty relationship to this day.
2 Ace
A powerful young psychic girl known only as "Ace" was abducted first by Project Cadmus then by the Joker, both of whom weaponized her telepathy. As if her life wasn't tragic enough, Justice League Unlimited episode "Epilogue" revealed her ultimate fate: her powers induced an aneurysm that would not only kill her, but everyone else for miles around.
Amanda Waller argued to the Justice League that Ace had to be euthanized with a Cadmus-developed weapon, and Batman seemingly volunteered for the task. When he reached Ace, however, he threw aside Waller's weapon, having never intended to use it; instead, he offered Ace sincere friendship and understanding for the first time in her life, staying with her until the moment she passed peacefully.
1 The Joker
"The Killing Joke" is not a story without issues, but the one note of the comic that remains worthy of commendation is the final one - the conclusion is the most concisely harrowing encapsulation of Batman's relationship with the Joker, and a fitting denouement thereof, because it illustrates like no other how their eternal struggle can never reach a climax.
After the Joker rejects Batman's offer of rehabilitation, he tells a joke about two men attempting escape from a lunatic asylum, a joke that sounds evermore familiar as it's read again and again. Once he delivers the punchline, the two adversaries share clarifying laughter - as author Alan Moore explained it - "the two characters [are] experiencing a brief moment of lucidity in their ongoing very weird and probably fatal relationship with each other, reaching a moment where they both perceive the hell that they are in, and can only laugh at their preposterous situation."