Suicide pacts are unusual, and experts say charging a survivor with murder for his counterpart's death - as Yiambilis is - is even rarer.
At Friday's hearing, lawyers battled over a defense request to dismiss the murder charge. Cepparulo could rule on the motion in the next few months.
But the judge's comments suggested he wanted more proof justifying the homicide charge. "Is there any evidence that he took certain steps to avoid dying or that he would live and his mother would die?" Cepparulo asked.
Deputy District Attorney Alan J. Garabedian said the evidence shows Yiambilis intentionally caused his mother's death when he turned on the generator inside the apartment and refilled it when it ran out of gasoline.
The fact that she wanted to die is not a defense, Garabedian said.
The judge swatted away that argument. "You have got to be kidding if that's your supposed evidence for malice in a homicide," Cepparulo said.
The judge also criticized prosecutors' decision to add to the case a second, seemingly contradictory, charge of assisting a suicide.
"You can't have homicide and assisting suicide," Cepparulo said. "Those two don't fly."
Garabedian told Cepparulo he believed the case was a homicide. But he said a jury could look at the evidence and decide the assisted-suicide charge was more appropriate.
"I don't know if that's the role of a prosecutor," the judge countered. "You can't say, 'I'll charge any crime and let the jury make a decision.' That's just wrong."
The judge's admonishments capped a hearing during which Yiambilis' attorney, William Goldman, read aloud portions of the seven suicide notes the mother and son had written.
"I love you - please understand why we left this world," Karen Yiambilis wrote to her daughter. "Gus and I were very unhappy. The negativity was too much for us to deal with anymore."
Yiambilis, who remains jailed without bail, used his cuffed hands to wipe his tears, and other relatives who attended the hearing cried as Goldman read the notes.
Yiambilis is the grandson of Nick Yiambilis, an immigrant who became one the region's most successful Greek restaurateurs, starting in 1960 when he opened the first St. George restaurant, and later the Midtown restaurants with a nephew.
During the hearing, Goldman also presented new evidence in his client's defense. He said the tape used to seal the apartment vents, doors, and windows - to keep the deadly fumes inside - contained 41 fingerprints, but none belonged to Yiambilis.
His mother's fingerprints were never taken.
"The record is completely void of any evidence [of homicide], because none exists," Goldman told the judge.