The three have the same meaning, restraining devices for prisoners, but in the US today, "handcuffs" is the only one of the three that is heard, and it's heard frequently in a police context; this is what police put on people they are arresting. "Manacles" and "shackles" might be seen in a literary context about the 19th century or earlier. Also, "shackles," especially, implies very heavy restr