I always pick the non-lethal route if given the option. As I've stated in another post about video game violence, I've just grown tired and bored with it over the years. I like having options that don't all boil down to "and then I killed him, so problem solved."
Now I'm not against it in games, like the OP said, it makes sense in games like God of War, or Borderlands 2, but when given the option I always take it.
The only time it slightly irks me is when the fact that you did or didn't kill anyone factor directly into the quality of ending you get. Like Dishonored and Deus EX: HR. Yeah, they give you some wiggle room if you have a low body count, which is fine, but I do admit, against my usual aversion to being an Achievement Getter, that "Pacifist" achievement in games does dangle in front of me a lot, and I want it. That's one of the few times where I will really bust my ass to try and get an achievement in a game, the non-lethal achievement.
In some games it's not even a big problem, like in Mirror's Edge. That game was so focused on avoiding conflict by simply parkour'ing past it, that the achievement was pretty much a sure thing. Other games though, it can be more of a challenge.
But yeah, rambling aside, I love non-lethal options, and happily take them when possible.
*Edit* I especially like it when the game rewards you for the non-lethal approach with bonus xp. Because if you ignore the badguys, depending on the game mechanic, you are basically missing out on XP, which means being stealthy and non-lethal can hamper your progression. So, at the end of the mission, you get a bonus xp chunk for not being seen or setting off alarms, to help mitigate that discrepency. I like that, like in DE:HR. It helps to encourage the non-lethal/non-combat/avoidance game style, where you don't feel like your missing anything.