Comes from video games where you usually can hit ~ (tilde) or other character to make a in-game console appear, usually sliding down from above or at least in the top half/third/quarter of the screen. Popularized by Quake and games from that heritage (like Source engine) I suppose.
Desktop equivalent is that you have a terminal available at a short-cut/button-press that will always show it but not fully hide the rest, no matter what other context you're in. Pretty handy.
