In Deja Vu, you can break into a house and poison someone while they're sleeping, and still win the game. The person still shows up in the ending epilogue, I believe. Hell, all the ICOM Simulations games have some pretty brutal death descriptions.
Rescue: The Embassy Mission, you can kill some hostages, not the best ending but I'm pretty sure you still kinda win on the lower difficulties. Took me a while to realize you're not supposed to shoot the non-moving silhouettes in the windows.
Kid Icarus has bare tits in the manual. On a monster, but tits are tits, right?
Don't forget the infamous microwavable hamster in Maniac Mansion.
Haven't played Double Dragon 2 on NES for a long time since I don't have the cart, but I know the arcade version starts out with Marion getting gunned down.
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Edited: 12/30/2015
at 05:13 AM
by Memblers