This is Always a hard topic since some games that where really bad have slipped under the radar or are quickly forgotten. Here are a few that pushed the limits but never seem to get there due.
Death Race (Arcade - 1976) - The great granddad of controversy games. years before mortal combat made headlines this one made headlines as it was the first where your goal was to simply run over people (based on the 1975 cult movie of the same name). Back in the day this was the first game that I became an expert at which might not necessarily something to boast about.
Robocop vs the Terminator (Genesis - 1994). Released during the Sega Genesis era and round the same time mortal combat was released and causing an uproar. Oddly enough even the regular mode was far more violent than Mortal combat but there was even a code to make it even worse (heads popping off and women enemies exploding into pieces) yet hardly a word was ever mentioned of this game.
Tecmo's Deception series (PS1 and PS2)- Not particularly gory but definitely brutal in tone. Killing off intruders with traps was always pretty cruel and satisfying but the sequel Kagero (Deception 2) briefly sort of upped the ante by actually allowing you to kill a kid (or maybe two?).
Hitman Series - Not sure why this was left out. Of course if you played the game like an pro (only killed the target(s) intended) there was not to complain about; however, if you wanted your own version of a Friday the 13th serial killer video game, then you could really rack up the body count.