Thinking about it, I might say that an assassin who worked *purely* for money might fit as a neutral character--especially if the money wasn't the key motivator. (There is of course the issue of "a tough job, takes more effort, more time, etc., should cost more", though.) That is to say, accepted any job, regardless of what side wants it done. A good character would take jobs that are in the best interest of the world at large. An evil character would take jobs that further his personal goals in the end.
That's not quite enough of a division, though. The other issues are the means and the side-effects. An evil character wouldn't worry about involving other people in the job (by which I mean, killing them, wreaking havoc, etc.) A neutral character should probably aim to perform the job with the most possible finesse--only the target dies. Aside from the fact that there is now one more corpse (which may have a serious impact), nothing has changed.
For the means, we get to the Assassin PrC a little. Using [Evil] magic is something a neutral assassin would avoid. If poison use is considered evil in your campaign, that would be out as well. If it's not, then it's not a problem.
So here we have a recipe for a neutral assassin. An assassin that kills not for personal glorification, but because it's a job, and he performs that job well. Done with appropriate methods, without undue impact on anything but the target.
A good image of this would be the Assassin's Guild in C.J. Cherryh's Foreigner books. Not only would I say they are neutral, I'd say they're lawful neutral. In fact, they *are* the legal system in many ways. They perform their jobs without regard for the reason that their lord requires them to perform the job. If they are not employed by a lord, the general public can hire their services. (And part of "they *are* the legal system" comes in here--it's reasonable for them to turn down a job if they feel the cause isn't lawful.) The organization might be good in a way--it's part of the framework of society, and keeps civil order--but the individuals are neutral. (And the cause of the lord they might follow isn't totally relevant--atevi loyalty ("man'chi") is a biological imperative, not a conscious choice.)
Not a perfect analogue, because of the strange qualities of man'chi, but an interesting idea.

Good books, too.