There are a lot of manga series about assassins.  Kazuo Koike has penned several, in fact, including Sanctuary, Crying Freeman, and Lone Wolf and Cub, one of the more famous series.   But there are many titles with assassins in them, a few that deal with killers of men, and a handful with an assassin character, who may be serious or a joke.  Sometimes the assassins are somehow benevolent, sometimes they're disturbed individuals, and sometimes they're just professionals.  But here are three series, all of them quite good, that deal with three different types of assassins.

Lone Wolf and Cub - Kazuo Koike and Goseki Kojima (28 volumes)

Honestly, I was a little taken aback when I started reading this.  I thought it was a fairly serious samurai action series.  And it is.  It's set in feudal Japan, and there's a lot of information about the political systems, contemporary ways of life, corrupt politicians, being a warrior, and things like that.  Setting that aside, the premise for the series is fairly bizarre.  Itto Ogami is the exiled and wrongly disgraced Shogun Assassin, and he takes his young son with him as he works as an unaffiliated assassin for hire.  But the greatest thing about this series is probably that Ogami actually uses his infant son as bait to lure his targets close enough to kill them.  Early stories involve Ogami leaving Daigoro out in the open so that someone passing by might walk up to him with some concern, at which point Ogami pops out and kills them.  And it only starts off that way.  It gets stranger and stranger as the series goes on.  We find out later that Daigoro is coming along with Ogami because, when given a choice between a ball and a knife, Daigoro chose the knife.  Hardboiled assassins look into Daigoro's eyes and can tell he's completely dedicated to the path into Hell, along with his father (there's a whole philosophy behind this).  Daigoro can charm ladies and run out of harm's way with the best of them, and sometimes find his father after he fails to return from a mission.  Aside from its over-the-top and completely serious nature, it's also still one of the best action manga money can buy.  Kojima has incredible, heavily inked artwork that is inspired by ukiyo-e, while still maintaining his own style and being perfectly legible and fluid during fight scenes.  He includes a lot of detail, and is quite good at drawing a wide array of weapons.  And Koike brings his usual amount of crazy into play, where the situations that Ogami has to get into, out of, or solve in each volume get increasingly more ridiculous.  This isn't as outright incoherent as Crying Freeman is, either.  The situations are fairly straight-faced and acceptable within the logic of the series, and not so ridiculous or extreme they take you out of the story.  For the most part.  But I've only read five volumes of it, and I know Koike has a tendency to... derail sometimes.  It is one of the classics though, in both Japan and America, and it is worth reading at least a little bit of it.  There's a couple different editions, but Dark Horse did finish the entire run, and enough copies exist that they shouldn't be too difficult to track down, but if you don't like scrounging for used books, they are currently republishing the entire series in omnibus form.

Gunslinger Girl - Yu Aida (15 volumes)

Here's another unusual approach for an assassin story.  This series focuses on several girls, all of whom have had terminal illnesses or were in fatal accidents.  After obtaining parental consent, the girls are healed and rebuilt as cyborgs by a private Italian organization.  They receive a brainwashing and re-education, and are then sent out as high-profile and very expensive "assassins," each with a male handler.  The theory being, I suppose, that nobody is going to suspect what appears to be a little girl with a cello case of being a murderer.  Given the appearance of the girls and the older male handler, I was reluctant to try this because it had a pretty high creep factor for me.  But... actually, this series is pretty engrossing, and handled fairly tastefully.  It's episodic in nature, with each story segment focusing on one of the girls.  Sometimes we learn a little bit about their background (which, for the most part, they either can't remember or don't care to), sometimes we follow them on a mission, but a big part of the series is also the relationship the girls have with their handler.  Again, it's not at all creepy or romantic, for the most part, and most handlers act as a big brother, surrogate father, or strict teacher, depending on the personality of the girl or the handler.  The girls look up to and depend on the handlers for a lot, and their relationship often reflects their psychological state and how well they can do their job.  Sometimes there are longer stories and a little bit of overarching plot, mostly concerned with a terrorist organization named Pandida.  There are some lengthy stories that give background and sympathetic backstory to the organization, but it frequently comes up as a thorn in the side of the assassins.  Some of the connecting threads also have to do with gossip about the girls, including one girl who killed herself before the start of the series, another girl who doesn't have a handler and stays in, another girl who is close to being decommissioned, et cetera.  It's got a pretty fascinating and diverse set of stories that it rotates through, and fortunately isn't a terribly lengthy series, either.  There is some action, but it's mostly about the lives of the girls and how being an assassin may or may not have a bearing on their pre- or post-brainwashing personalities.  It's an interesting take on the assassin position, to be sure.  There are a handful of volumes from the now-defunct ADV Manga, but Seven Seas license rescued the series and released it as a series of omnibuses.  The final volume is coming out in July.

Golgo 13 - Takao Saito (167+ volumes)

This is really THE assassin comic.  Duke Togo (real name unknown, alias Golgo 13) is the world's best assassin.  Period.  His true background and any personal details about him are completely unknown.  You can hire him for an outrageous sum of money, if you already know how to do so.  When you meet with him, there are several conditions, such as he never shakes hands, never has his back to the door, and can turn down a job at will.  He will never meet with you again, and you can assume that he takes care of his target, as he has a 99% success rate.  Each volume usually has two stories, and each story ends with an absolutely epic termination of Togo's target with one shot.  The stories are unconnected (so unconnected, in fact, that all of the material published in English is nonsequential and is from many points along Golgo 13's 44-year run).  Half of the appeal to the stories is the character of Duke Togo himself.  He is completely unchanging, and part of the fun is that no matter what crazy situation he winds up in, he finds a way to obtain a gun and kill his target.  No matter what.  He is completely stoic, and keeps a straight face regardless of the situation.  Most of the other half of the appeal are the situations, which are usually heavily political, but the stories are told in such a way as to be interesting.  Sometimes the stories deal with contemporary events (like in English volume 4, where we find out the true story behind the death of Princess Diana), and sometimes the situation is more vague and disconnected from reality (such as one of the English volumes from the 80s, which is about a Saudi prince who flees to his home country to escape a murder charge in NYC).  The stories are action-packed, and always very exciting.  Sometimes it's fun to see just how Duke Togo will get close to a target, like one story where the Vatican has been keeping a Duke Togo look-alike as a cardinal just in case they needed to hire him, another where he flies pieces of his gun in on carrier pigeons, and another where he snipes a satellite from space.  My favorite features Golgo 13 commiting the final kill during the call to prayer, when he knows his target will be reachable through the window of a building when he sits up during the prayer, and he ricochets his bullet off another building to kill him.  This series is just a lot of fun to read.  There have been many different editions through the years, including a recent "13 volumes of Golgo 13" release by Viz, 4 volumes in English from a Japanese publisher in the 80s, and a handful of stories in loose issues from Viz, Vic Tokai, and Takao Saito's own company.  I recommend volume 4 of the recent Viz release along with the older volume titled "Galinpero."  Those two volumes might be among my favorite comics ever.