The Penguin
The Penguin was born as a deformed child named Oswald Cobblepot, and was bullied as a child because of his lack of height and bird beak shaped nose. In several stories of the Penguins origins he was made to carry an umbrella as a child by is over protective mother because his father died of pneumonia after being drenched in a downpour.
However Christopher Nolan has gone on record and said that some villains of the Batman universe wouldn't work well on screen, the penguin being one of them.
Catwoman
Originally know as Selina Kyle a woman who turned to the life of crime because of her love for diamonds, however over the years she has been known to have been a beaten housewife, a dominatrix and a prostitute. The later would fit more into the Dark Knight's universe as her attire would be easily explained in this way.
Having said all that David Goyer as expressed that both him and Nolan would rather use a villain that has not yet been seen before on screen in any batman franchise, however I wouldn't rule out the possibility of Catwoman making an appearance, as TDK made references that Batman's suit would be able to take an attack from a 'cat'.
The Riddler
Forget Batman forever and Jim Carrey's portrayal of the character and let's start fresh. Edward Nigma also known as Mr E or E.Nigma started solving puzzles as a young child when one of his school teachers announced that if one of the pupils were able to solve a certain puzzle then that person would win a prize. Later that night young Edward broke into the school and figured out how the riddle worked. When he won the prize by cheating, Edward grew up needing to feel this satisfaction again and again, over time his thrill of the challenge escalated to the point that he felt the only person worthy of challenging him was Batman.
Fans have already started name dropping stars such as 'Casey Affleck' to play the green menace, however this is just speculation and no names have been linked to the project as of yet. Another point that I haven't seen many people pick up on is the employee Coleman Reese which could be looked at as Mr. Reese (mysteries) maybe just a coincidence maybe not.
Harley Quinn
Dr Harley Quinn a villain not as popular to the non fans of comics would be an excellent addition to the Batman 3 franchise, but we would drop the Dr and just have her as Harley Quinn. For obvious reasons the Joker will not be present in the third movie of the franchise but that doesn't mean the events of The Dark Knight wouldn't inspire an copycat killers, just as Batman Begins inspired normal civilians to dress up as the caped crusader.
Deadshot
Fans of the comics will also not recognise this name, however Deadshot once a good guy turned hired gun could be an excellent choice for a villain. With Batman now on the run from the police and pretty much has destroyed the mob it would make sense that the best hired gun in the business to be called in to assassinate The Batman.
Could he work in Nolan's world? Defiantly as Batman has inspired people to try to become heroes but Deadshot would just use this angle to gain everyone's trust and then gradually try to take out Batman and then become king of the underworld like in his previous incarnations in the comics.
Two-Face
Yes he died in TDK, but if Nolan wanted to bring back the character via anyways possible we wouldn't object. However it seemed the character has lived its purpose, but I'm sure if Nolan wanted, two face could still be an interesting nemesis to the dark knight.
