The Batman Adventures: Mad Love winning an Eisner Award for "Best Single Story" in 1994. Frank Miller even declared it the best Batman story of the decade.
In Batman: Gotham Adventures #1, Alfred knocking out the Joker from behind when he invaded Wayne Manor.
Of corse, this was only after Joker beat Batgirl unconscious with just a fake arm.
Alfred takes down three kidnappers while handcuffed to a chair in Gotham Adventures #16. His rescuers burst in to find him serenely playing a game of solitaire.
According to Batman, that's the twenty-eight time Alfred is kidnapped. Every time, Alfred single-handedly took down the kidnappers.
Gotham Adventures #26: Batman's found himself caring for a baby that's wanted by villains, and can't risk leaving him alone, and so goes out to fight crime anyway, with the baby under his arm. A bunch of crooks aren't impressed... at first.
Batman: You know who I am. You know what I can do. But I am holding a small child here. And if you make me do anything that could possibly endanger this baby... You will be very, very sorry. *pause* Forever.
And the thugs immediately surrender their weapons. The moment is broken, though, when they have to tell him he's holding the baby wrong!
The Joker and Harley get one in Batman Adventures #3. After a story arc in which shock therapy by Arkham turns Mr. J into a pacifist, Harley finds herself less attracted to him. During a climactic confrontation with Batman, she gets fed up with her puddin's groveling. In an attempt to snap him back to his old self with jealousy, she tells him that she wants to be with Batman now and even kisses him (much to the Dark Knight's shock). Joker responds by beating the living hell out of him. Batman does overpower him and win in the end, but seeing anybody manage to catch the Goddamned Batman off guard is quite impressive. All for the love of his Harley.
Commissioner Gordon: Be quiet, Joker. Nobody believes you - You're a raving lunatic. Joker: A homicidal lunatic, thank you very much. Harley: Didja hear that, everybody? My boyfriend's back!
Also one for Arkham Asylum: even if it didn't last, they were actually able to pacify the freaking Joker!
Clayface gets one in Batman Adventures #14. During a climactic fight with Batman, Clayface falls into a concrete mixer, causing his body to mix with concrete and solidifying him. The final shape that Hagen takes before dying is that of his childhood hero the Gray Ghost, living on as a statue of his idol.
Scarecrow, even though the lead up was tragic, gets his own in The Batman Adventures Annual #1. He manages to break free from Arkham and manages to change his life around, teaching under a new name at a university and even has a brilliant female student he's proud of.. But then the student's Jerk Jock boyfriend ends up beating (or possibly raping) her, traumatizing the girl. End result in possibly the most personal and Papa Wolf related way: Goodbye Dr. Crane, hello Scarecrow.