When I first saw this scene I was surprised that Mind Palace Moriarty listed Irene as one of the people who would cry over Sherlock’s death (I figured it would make more sense to include Molly in that slot). However, after mulling it over, I concluded that there’s a deeper meaning to it. When you consider who these people are to Sherlock or what they symbolically represent, this list has a pattern.
First, Jim mentions Mrs. Hudson. Mrs. Hudson has always been like a surrogate mother to Sherlock and, up until S3, she was the only mother figure in Sherlock’s life that we knew about. So you could say that Mrs. Hudson is symbolic of parental love and affection. Next on Jim’s list are Sherlock’s actual parents; they are the literal representation of parental love.
Then, the camera angle changes—this change further emphasizes how everyone is paired off (Mrs. Hudson/Sherlock’s parents, Irene/John)—and Jim lists Irene who, as many others have pointed out, is often the symbolic representation of romantic love and sex. So, if we continue the pattern of symbolic love followed by literal love, what does John represent?