Foe Yay: The Riddler's attempts to get Batman's attention include making dinner for him (lobsters, no less). While wearing a "Kiss the Genius" apron.
Batman and Joker, as usual. In Batman: Gotham Adventures #1, Batman needs to keep Joker in the Batcave, since there's now a reward for Joker's death. Joker's response:
Joker: We're moving in together? That's a big step. I'm not sure we're ready.
Not a page-and-a-half later,◊ Nightwing shows up. Joker asks if he has any idea what time it is, saying that "your father [Batman] and I have been worried sick!"
"Funny Aneurysm" Moment: The first Annual features a humorous little short story showing how easy it is for Harley to drop everything to go back to the Joker's side. It becomes a lot less amusing after reading Mad Love.
Hilarious in Hindsight: In Gotham Adventures #15, Robin rattles off a list of what he thinks Bane might be trying to do with the money he's stolen in a series of daring daylight robberies in the financial district. This includes buying a nuclear weapon, a local sports team, Bruce Wayne's company, or an expensive operation for some medical condition he might have. These elements all figure prominently into the plot of The Dark Knight Rises, although not necessarily the way Robin was thinking.
Les Yay: In "Mad Love", after Harley's been thrown out a window by The Joker, Renee Montoya cradles Harley in her arms, with a worried look on her face. While there's nothing romantic about it at the time, considering that Renee later came out as a lesbian and Harley later became close with Poison Ivy (in a relationship sometimes hinted at, but never explicitly stated to be sexual) puts a whole new light on it years later.
Moral Event Horizon: Two-Face finally seems to be making a recovery into sanity and happiness...so the Joker goads him into thinking that Bruce and Mrs. Dent are having an affair, and even has Harley convince a tabloid that they're engaged. So of course Two-Face snaps.
The Woobie: Surprisingly, the Riddler. After escaping from Arkham in Gotham Adventures, he decides he'll hide in a penthouse and send Batman clues to other people's crimes to satisfy his compulsions without incriminating himself like he normally does, because he hates hates hates Arkham and never wants to go back. Unfortunately, all those clues come together to make a clue to the location of his hideout...and he did that subconsciously.