Twenty-four-year-old Ryan Lane disappeared in February after a call that police believe was intended to lure him to a northwest neighbourhood.
His remains were found in June during the search of a large area northeast of the city.
Sheena Cuthill, the mother of Lane's daughter, stood in the prisoner's box, while her husband, Tim Rempel, and his brother, Will Rempel, were on closed-circuit TV.
All three face first-degree murder charges and are next to appear in court Dec. 21.
Police believe a child custody dispute was the motive behind Lane's slaying.
The cause of his death has not been released.
Police believe Lane received a phone call the night he disappeared from someone offering to help him in a custody dispute, but his father said his son wasn't in a custody battle.
Lane's mother, Lorraine Jackson, has said her son wasn't a threat to anyone and the family will never get over what happened.
"Ryan will never have a chance to know his daughter, to find true love, to grow old with us," she said at a news conference Nov. 23. "Everything is gone for him now.
"And we have to carry on?''