"Perchance to Dream" consists mostly of an extended dream sequence created by the Mad Hatter to keep Batman trapped in a dream world. After Batman finally wakes up into reality, he looks at the elaborate head rig created by the Mad Hatter, and calls it "the stuff that dreams are made of".
In "Off Balance", Batman asks Talia whose side she is on. "That would be telling" she replies. Almost every episode of The Prisoner (1967) started with that dialogue.
At the end of "Jokers Wild", the inmates in Arkham are watching Bugs Bunny cartoons.
To It's the Great Pumpkin, Charlie Brown, where one thing Sally said to Linus in the pumpkin patch was, "If you try to hold my hand, I'll slug you!"; near the beginning of "Joker's Wild", in the lounge at Arkham Asylum, Joker cozies up next to Poison Ivy, and teasingly says, "If you hold my hand, I'll slug you!"
"Harley's Holiday", Harley Quinn, upon returning to Arkham, says the line, "Home again, home again, jiggity jig." It's a reference to the scene where one of the toys says the same line when J.F. Sebastian comes home with a woman in Blade Runner.
In "The Clock King", the streets have the names from various comics and animation artist who worked at Batman: Keith Weesner, Jack Schiff, Jerry Robinson, Norm Breygfole, Alex Toth, and Kurt Busiek.
In "Harlequinade", when Harley does her impromptu musical number she instructs the orchestra that she will be singing in the key of A flat, as Lina does for her impromptu musical number at the end of Singin' in the Rain (and in very nearly the same nasal voice).
In "If You're So Smart, Why Aren't You Rich?" Batman immediately deduces the Riddler's reference to a lyric from the Oklahoma! song "Oh, What a Beautiful Mornin'." Robin fails to get the reference to "corn as high as an elephant's eye," and Batman has to explain it to him.