I'm looking for an assassin or spy type of manga. The protagonist is preferably female, who uses mostly her wits, as well as her fighting techniques to complete the mission or running away from hitmen. The story should be episodic, at least for the first few chapters. I don't want the manga to be mostly violence, but there should be a kind of ingenious strategy or quick thinking on the protagonist part. Oh, and she should usually work alone, except for special cases. Is there a manga that could fit all my specific descriptions?

You could probably find some stuff here... :

http://www.mangaupdates.com/showtopic.php?tid=7905&hl=spy
http://www.mangaupdates.com/showtopic.php?tid=15522&hl=spy

http://www.mangaupdates.com/showtopic.php?tid=7022&hl=assassins
http://www.mangaupdates.com/showtopic.php?tid=14250&hl=assassins
http://www.mangaupdates.com/showtopic.php?tid=9841&hl=assassins

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I've checked most of the manga in the threads, but the only one that comes close is Tista, and it doesn't fit in terms of the personality of the main character. What I'm looking for is a heroine, that has a spy or assassin type of job, looks and acts cheerful but could be ruthless. I want it to be action-based, with conspiracy theories, and it's alright to have some light scenes, due to the heroine's nature.

It's an anime, but try Madlax. =)

If you've ever thought or said "Nice Guys finish last" and really meant it, then you should probably read this LJ post by DivaLion. It's incredibly insightful whether you're male or female.

From a bumper sticker I like:
"If you're gonna ride my ass, at least pull my hair."

Beside the work alone part, Gunslinger Girl kinda fits.

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

There's always Golgo 13

lady snowblood, it fits iirc all of the requirements

Okay, um... Closest I can think of in terms of job and personality is Young Gun Carnival, but the girl is not really a main character compared to the male lead.
Bloody Cross could be one I guess, but it more like the girl and guy are acting as equals; flirting and double-crossing one another.

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9 banme no musashi is the first one i thought of.

Seconding Lady Snowblood, it fits the bill exactly!

C.A.T.

[color=#ff0000]"“That's the difference between me and the rest of the world!
Happiness isn't good enough for me! I demand euphoria!” "[/color]

oh yeah you could also try white dragon. assassin is not strictly female, since he can morph his body into male one aswell.

Ghost in the Shell
(I've only seen the start of the anime, and the assassin doesn't work alone... But it kinda fits?)
Also Gunslinger Girl, but I think this one has already been mentioned.

Crying Freeman or Angel heart(although she is an ex-assassin) maybe

Thank you, for all the reply, but none of the manga came close to what I'm looking for. Maybe I should put it as a Bourne Identity manga version, but with a female protagonist?