Well, we know about The Joker and Two-Face, so no need to include them in my wish-list. But here's some other villains I'd like to see. Not saying they're likely to appear, and since I hope this series doesn't extend past three films (end it on a high note with an astounding trilogy), maybe it's better they don't. But still some ideas:
THE RIDDLER
This is a villain that I'm holding out a faint hope might end up being in "The Dark Knight", played by Anthony Michael Hall. I'd have The Riddler be as he is in "The Long Halloween" and "Dark Victory": a sleazy informant who Batman puts the scares to for info. That way, he can have a good number of scenes, but at the same time doesn't need a lot of screen-time devoted to him to have a satisfying, complete role in the film.
POISON IVY
Of course, a lot of the "toxic blood" and "control over plants" stuff would probably have to get dropped for Poison Ivy to work in Nolan's Batman franchise. I'd introduce Poison Ivy as an assassin who uses a variety of plant-based chemicals to manipulate and/or kill her victims. Theremones, halluciginents, and of course poisons. Her trademark weapon can be the lethal poison lipstick. But she can maybe have a poison-tipped knife at her disposal for combat situations. They could possibly play up the psychotic element of the character by making her fanatical about plants, go for the whole barefoot-naturist look she sometimes has going in the comics.
KILLER CROC
Remember in "The Long Halloween", how after he's scarred, Harvey Dent flees to the sewers, and meets Solomon Grundy? Well could they maybe recreate this in the movie, only with Croc replacing Grundy? Some may think Croc is too "out-there" for the Nolan films, but they're probably thinking of his more recent appearances, where he has become a walking, talking crocodile. If Nolan and co were to base his looks off his earlier appearances, where he actually looked like an African-American man suffering from a horrifying skin-condition, then they could be onto something. He doesn't need much backstory, just that he's lived in the sewers for a long time, and that - like Grundy in TLH - he establishes a trust and connection with Two-Face.
HARLEY QUINN
In terms of backstory, they could keep Harley Quinn's largely intact. Arkham intern who falls in love with The Joker, and breaks him free. Again, it wouldn't really need to be a huge part, I doubt she'd have any screen time seperate from The Joker. But sadfly, the costume would have to change. Possibly maintain the white makeup, but give her a dark red dress? Create a twisted "Joker's Bride" vibe.
Like I said, however, I only imagine this franchise stretching for three films. And its HIGHLY unlikely all these characters (along with Two-Face and The Joker, and possibly Scarecrow) could all squeeze into one film. UNLESS, the whole story of the third Batman film is reminiscent of Dark Victory, with Two-Face assembling an army of "freaks" to take over Gotham City, wiping out the gangsters and replacing them with the crazies once and for all.