I feel bad about killing anyone who's named in Skyrim. Just because the city feels slightly more... empty. Even the bastard Nazeem and that demon-child Frodnar have their place in the world of Skyrim. Of course, any Guard, Soldier, Bandit, or random NPC of any sort is fair game. I usually get my sneaking skill up by murdering the guards patrolling the Whiterun countryside. It's fun to murder them and dump their bodies in the river knowing that they'll respawn soon enough. Then again, the NPCs that TRULY deserve to die like the Thieve's guild (why can't I wipe them out like the Dark Brotherhood? Thieves are scumbags), Maven Black Briar, and the enemy generals are apparently highlanders. And why can't I just piss over to the enemy stronghold and kill Ulfric or Tullius during the civil war questline? In New Vegas, I infiltrated the Legion camp and assassinated Caesar in the process of doing the NCR questline. I think New Vegas is one of the only games where you can truly kill everyone. The only invincible NPC's that I know of are Yes Man and... that's about it. That's one of the things that really makes my butt sore in Skyrim.
I also felt bad about killing Dante Moro in AC2. The dude was betrayed and left mentally crippled, had his wife stolen from him, and was made into a personal slave by Marco Barbarigo. Dante was just a man-child who was dragged into the conspiracy against his own will, and he even betrays the Templars on his deathbed. I know that Ezio doesn't really know Dante's full story, but I still wish there was an option to spare Dante and hand him over to Bartolometo to join the good side. And the letter from his wife... I almost teared up for the first time in gaming.
I also felt bad about killing Dante Moro in AC2. The dude was betrayed and left mentally crippled, had his wife stolen from him, and was made into a personal slave by Marco Barbarigo. Dante was just a man-child who was dragged into the conspiracy against his own will, and he even betrays the Templars on his deathbed. I know that Ezio doesn't really know Dante's full story, but I still wish there was an option to spare Dante and hand him over to Bartolometo to join the good side. And the letter from his wife... I almost teared up for the first time in gaming.