I'll attempt to explain this as best as possible. What I essentially want is a character that is completely and utterly devoid of morals. That character can't even imagine the concept of guilt. Now I'm not talking about a cold-blood killer (they often turn out to understand what they're doing, but don't care or have become numb), but more like an innocent and childish character that wouldn't hesitate to kill an annoying person.

In a shounen battle manga, the character would be the type that would say something like "Why? I didn't do anything wrong." with an innocent face after an attempt to kill a person.
Examples:
Usotsuki Mi-kun to Kowareta Ma-chan: Totteoki no Uso: Female Protagonist

It can be any genre and the character doesn't have to be the protagonist. No yaoi or shounen-ai please! It's okay to say any manga that's already in my lists.

First things to come to mind are Darker than Black in which the contractors are all devoid of morals due to their... 'condition'.
and Monster, in which the eponymous monster is the epitome of sociopathy.

In Mirai Nikki, Yuno will do whatever she needs to, to keep Yukiteru safe, and has apparently no understanding of right and wrong past this point.

In Madoka Magica

BIG spoiler ahead

Kyuubey has no emotion whatsoever, and is completely unable to understand the distressed (to say the least) reactions of the girls after numerous nightmare-fuel revelations about what being magic girls really means.

And Deadman Wonderland has several pretty f*cked-up characters, who have a childlike approach to torturing and killing people.

Pretty sure Ilya from Fate/Stay Night is exactly what you asked.

Gunslinger Girl Not sure if it can be considered what you asked, but it applies to all the girls of the manga, so you should at least check it out. Example: Triela after killing an enemy

http://www.batoto.net/read/_/68870/gunslinger-girl_v5_ch27_by_manga-sketchbook/34

What I like in Trivial Pursuit style. Pick your category:[img]http://i379.photobucket.com/albums/oo233/Reid4891/Manga/trivia-1.jpg[/img]

Issho ni Neyou yo

I don't know if he could be driven to murder, but I seem to recall him being jealous over something and getting violent, and responds to his scolding as a child might (i.e., "He stole my toy so I hit him")

then again I think he does feel guilt at some point. Sorry, ignore!

Go to work, send your kids to school;
Follow fashion, act normal;
Walk on the pavement, watch T.V.;
Save for retirement, obey the law.
Repeat after me: I am free.

Battle Royale - one of the students cannot feel anything due to a hit on the head, and another student have a pretty rough childhood.

Dorohedoro - i dont know if this qualify, because everyone in this world do not have a concept of killing = bad. it is a quite depressive world where they need to gain favour from the devils. but, its a fun read!

MW - its categorized as 'shounen ai', but i think you can still read it because its not about that, its about the sociopathy of one of the character. its written by tezuka osamu, so you know he never go for cheap thrills!

Freesia - he's just crazy. i dont know why, but he just dont feel anything, killing anyone, and dont even care watching someone got raped. i think something to do with the war. and he's the protagonist.

Franken Fran - fran dont kill people, she save them. but whether or not that's a good idea is debatable because she may turn you to a caterpillar or transplant your dog's brain to an old man in an attempt to 'save' life. its either her moral compass is broken, or she have an entirely different compass than regular human.

Anne Freaks - cant remember much, but i think anne is a brainwashed terrorist.

Fire Candy - the protagonist is a doped out sadist.

Narutaru - children with crazy superpowers. of course they do crazy stuff, they dont have the capacity to think it through.

ES - a clone with mental powers, but raised without a moral compass

Thanks guys. I've already read Battle Royale, Dorohedoro, Franken Fran, Mirai Nikki, and Deadman Wonderland. The rest I'll check out. Are there any more mangas like this (I'm a fast reader 😀 ).

Some excellent examples of what I want:
Mirai Nikki:female protagonist
Fate/Stay Night: Illya
Utsuro no Hako to Zero no Maria (Novel) :Spoiler

Kokone is almost the epitome of what I want. Shes overly cheerful and childish, but it's revealed how broken she is, even though she hasn't actually done anything yet.

Franken Fran doesn't really fit. Although Fran is innocent, she's not really childish or playful, so it doesn't have as big an impact when she does something cruel. Dorohedoro is the same.

If you're ok with novels (I think so since you mentioned Hakomari) there is also Youko from Gekkou (novel) who fits very well (imho more than Kokone). It's a nice novel even if it's not as good as Hakomari (but really, is there anything better than Hakomari? I doubt so).

What I like in Trivial Pursuit style. Pick your category:[img]http://i379.photobucket.com/albums/oo233/Reid4891/Manga/trivia-1.jpg[/img]

Takano Miyo: Higurashi no Naku Koro Ni, you have to be in a few chapters before realizing the little angel is twisted.