Gordon says, "Five dead, two of them cops." A definitive answer is impossible. Christopher Nolan, when asked about an answer during a Blu-Ray Live Event, responded "I will answer this question one day. But not today." Here is a list of who he could have meant:
The cops guarding Harvey Dent at Gotham General Hospital. One cop radios a second cop, who is guarding Dent's room. The guard cop does not reply, so the first cop goes in to check out the situation. The Joker shoots him and presumably has already shot the guard. That's two cops right there and it's possible that Gordon assumed that Two-Face killed them when he left the hospital not realizing it was The Joker.
Detective Wuertz. Killed in the bar.
Detective Anna Ramirez. While Two-Face lets her live, he knocks her out. She would have been missing. Gordon, knowing she's the one who drove Rachel, might have assumed she was dead. Or, less likely, Dent inadvertently killed her - although he intends to let her live, she could have been severely injured (e.g., head striking pavement) after being knocked out by Dent, and subsequently died.
Maroni's bodyguard. As soon as Maroni walks out of the building, and then walks around to get in the passenger side of his car, look to the left of the screen on the driver's side of the car. The bodyguard standing there is grabbed and pulled off-screen. (It's very fast and very quiet so don't take your eye off that guy.)
Maroni's Driver. Shot by Two-Face while driving along the scrapyard.
Salvatore Maroni. Not certain. Two-Face flips his coin and spares Maroni's life. He flips his coin again and tells Maroni, his driver isn't as lucky as he is. Two-Face puts his seat belt on and shoots the driver, causing him to crash and flip the car. While Two-Face walks away from the crash unscathed, we never find out what happened to Maroni. We can assume he was either killed in the crash because he wasn't wearing his seat belt or left Gotham and went into hiding afterwards; either way, he isn't in The Dark Knight Rises
Harvey Dent. Gordon could have meant Dent himself. Because in The Dark Knight Rises the public is under the impression that Batman murdered Harvey Dent in cold blood. It is never mentioned who else that Batman had supposedly killed.
Bartender. A far-fetched theory, but here it is. When Two-Face went into the bar to kill Wuertz, the bartender went to the bathroom. Seconds later, we hear Two-Face walk out of the bathroom. Two-Face might have also killed the bartender to get rid of a witness. Note that Two-Face always obeys the flip of his coin no matter who the person is or what they might have done wrong. If this did happen, the reasons the scene might have been cut are: it was too violent for a PG-13 film; it was too early for Two-Face to kill an innocent person (it would have been his first murder); Christopher Nolan wanted him to be a tragic character and therefore wanted to focus on him taking revenge on the people who ruined his life, rather than on him killing an innocent bystander.
Cop guarding Gordon's apartment. Also a bit far-fetched, but when forced to call Barbara Gordon, Ramirez refers to cops that are guarding the Gordons, and tells Barbara that they're not to be trusted. After letting Ramirez off, Dent might have killed them in order to ensure that they didn't stop the Gordons from leaving. Note that during the phone call, Ramirez stated that she could distract the cops long enough for the Gordons to leave - but Dent then strikes her and presumably knocks her unconscious. If so, then Gordon is not referring to Wuertz - implying that Gordon did not know Wuertz had been killed.
However, since Gordon was in the observation room during the interrogation scene, where the Joker told Batman "You didn't disappoint; you let five people die," fans could argue it could be the five people the Joker killed: (1) Brian Douglas, "a Son of Batman, " (2) Judge Surrillo, the judge presiding over the mob trail, (3) Commissioner Loeb, the man in charge of Gotham P.D., (4) Patrick Harvey, Gotham police officer, and (5) Richard Dent. The flaw in this argument, as far as comparing this to Gordon's final statement to Batman after Dent's death, is that it's a matter of record that the Joker killed these other people, or had them killed in league with Maroni, and Batman's "letting" them die was simply a matter of Batman not turning himself in and revealing his true identity, at which point the Joker would have retreated (though Rachel thinks not). Gordon is referring to people who have died after Dent's disappearance, and whose deaths might be traced to Dent. And remember that by that time, Rachel was already dead, which would have upped the Joker's death count to six.