Sunday Funday is a Christian NES game about a kid trying to get to Sunday School, while apparently every non-church-going person in his way tries to kill him before he can get there. Also, you aren't allowed to play the game peacefully; in order to advance much of the time, you have to kill everyone in the stage, sometimes violently with explosives. It's no real stretch to say that the game is, unintentionally or not, trying to teach kids that non-Christians are the enemy and must be destroyed.
In Chocobo's Dungeon you can kill enemies by kicking bottles at them, yielding you a bottle of red liquid. The implicstion being that the cute little birdie just bottled up his victim's blood. What's worse is he can drink it.
Imagine being a soldier in a unit, all of whom are traveling cautiously through the woods in a deep fog. You are ambushed by a massive gray blob that, before you can even act, overwhelms and devours you instantly. That was the fate of the poor Infantry unit in Advance Wars Dual Strike that was trapped by the first Oozium unit encountered in the game.
Star Fox Adventures: In DarkIce Mines aboveground, there's an area that you can't go through on foot. You can go through with a Snowhorn, but you have to keep walking over Alpine Roots along the way or his energy will run out and you'll have to start over. After arriving at your destination, you use him to do one thing and then leave him at the platform. Okay. Now what? There's not much there, so I'm sure he'd want to go back at some point... except he already ate most, if not all, of the roots along the way! Now, maybe they'll grow back, but who knows how long that'll take. Hope he can live on Magic Gem plants...