Mr Justice Barry White told the jury they must acquit Joe O'Reilly if they consider that the account of events given by him or his alibi-providers, Derek Quearney or Joseph O'Shea, "might reasonably be true".
"Even if you reject the evidence given by Mr O'Reilly, Mr Quearney, and Mr O'Shea, that does not prove the guilt of Mr O'Reilly," the judge said in his charge to the jury.
"The State still have to prove his guilt on the evidence in this case."
Having outlined the legal principles involved in the case, Mr Justice White said the jury were left with the question of who killed Mrs O'Reilly.
He discussed what was meant by circumstantial evidence.
He said: "circumstantial evidence is evidence surrounding circumstances of an event." He added: "You don't have any direct evidence as to what happened but there's evidence of circumstances which happened around the event which invite the jury to take a certain view. In this present case, the State are relying heavily on circumstantial evidence."
He quoted another judge who said: "there may be a combination of circumstances, any one of which may raise no more than a mere suspicion but taken together, they may raise a conviction of guilt with as much certainty as human affairs can admit."
He told them that "circumstantial evidence is evidence that points inevitably to the guilt of the accused man, to the exclusion of all other reasonable explanations". He said the State was saying: "there's a combination of circumstances, that when you put them altogether, points to the guilt of Mr O'Reilly and excludes all other reasonable explanations."
He said it was up to the jury to decide whether or not the case had any weight: "You will have to see whether you can combine the various strands or whether the strands can't be woven into the rope."
The judge then summarised the evidence of the 144 witnesses in the case.
He also told them he viewed some of the evidence as insignificant. Among the evidence he viewed as such was that given by farmer Mr McNally, a neighbour of the O'Reillys, who said Mr O'Reilly told him the red car Mr McNally had seen on the morning of the murder had been ruled out.
He also said he thought the evidence that Mr O'Reilly told Helen Reddy that Rachel had not been sexually assaulted was also insignificant, as it might be reasonable to assume that Mr O'Reilly took into account that Rachel was found fully clothed and that it might be just as easy for him to assuage her fears.
Similarly, he thought the evidence that Mr O'Reilly told Jackie O'Connor that he was being framed was also not that significant because as soon as somebody's spouse dies in suspicious circumstances, "the spotlight is likely to fall on the remaining spouse".
Relating to the letter found in the coffin in which Mr O'Reilly referred to something only both he and Rachel O'Reilly knew, the judge said there may be many "skeletons in the closet" among married couples and that it didn't necessarily refer to him murdering her.
He also said that that quote must be considered in context and that it was not Mr O'Reilly who suggested putting the letters in the coffin in the first place.
As far as the insurance was concerned, he said he thought that was also irrelevant because married couples have to have life insurance to get a mortgage. "Courts don't operate on speculation," he said.
They must approach the case "coldly and dispassionately." He told them that although he may accept a majority verdict at some point in the future, they were firstly to try to reach a unanimous verdict.
He also urged them to listen to one another but not to be swayed by others if it did not sit with their conscience.
"Be prepared to stick to your view if that is what your conscience tells you," he said.
At 5.50pm, the jury availed of their right to have parts of the evidence read back to them when they asked Mr Justice White to repeat the evidence of Derek Quearney and Det Garda Jim McGovern.
The jury resume their deliberations today.