The most shocking gory moment in Star Trek has to be the TNG episode where Lt. Cdr. Dexter Remmick is revealed to have some space slug inside his body. I don't think they've matched that yet for over the topness.
Oh yeah, until Trek melts another guy's head bigger than life, front and center, alone in the shot, that scene will always be the hands-down goriest.
Nothing in Trek matches the scene in Total Recall where Arnold Swarzenegger's character and the guy he was chasing are on the surface of Mars as their bodies expand due to vacuum. If I recall (only seen it once), the head on the guy he was chasing actually explodes while Arnold's eyes just bulge out of their sockets. Still pretty gruesome if you're 11.