taken from my guide's itemcyclopedia:
skull emblem: found after defeating the skull demon in “the first boss”
soul emblem: buyable at the auction in the underground city (in “saving the master”)
star emblem: earned after following the bull or lizard route in “the war ends - the war (part 5)”, OR after “wizardsss always get the last word”, by talking to Nauxus in the evening, only if he had 3 or less suspicion points; given/found on Selye in the Selye route after fighting him
still, some will be lost and found again, and not all of them are in the game yet