As a primary note, just as Neil alluded to: we are talking about 
writing about revenge and 
how it should be portrayed, not whether we should do so.
Romans 12:19 wrote:
Beloved, do not avenge yourselves, but rather give place to wrath; for it is written, "Vengeance is Mine, I will repay," says the Lord.
Deuteronomy 32:35 wrote:
Vengeance is Mine, and recompense; Their foot shall slip in due time; For the day of their calamity is at hand, And the things to come hasten upon them.'
For more, follow: 
http://www.openbible.info/topics/revengeThese are two Biblical quotes often dealing with revenge. They both 
seem to shut down any idea that revenge is ever a lawful reaction to provocation. Another excellent point is to consider Jesus' example, not taking vengeance on those who physically harmed him, and on the whole human race that attacked him by sinning.
And another point against revenge: Love your enemies. Can you love them when you send them to Hell the expressway (presuming that someone you would want vengeance on is unsaved)? You cheat them and God of any chance of redeeming them. And God is not willing that any should perish, but that all should come to repentance.
That leaves vengeance in a pretty rough spot. It would seem to make it almost a lie to portray revenge positively. And yet...
There are arguments in favor of vengeance. We could consider the argument based in, though not dependent upon, dispensationalism (nobody sue me). Basically the idea is that after the Flood and until approximately the Exodus God had instituted "Human Government" as the way of working justice on earth. Many ancient governments allowed this sort of vengeance seeking (Inigo Montoya style).
Parallel with this thrust is the idea of cultural differentiation. In some cultures it is customary for vengeance to be pursued. (I can't remember which specific ones at the moment).
The best argument though, is that of justice, the root behind the first argument and in tandem with the second argument. How is justice to be served? Consider this scenario based in recent events:
Months ago Americans experienced the "Fort Hood Shootings" where some guy in our army shot a lot of other people in our army. Suppose then that he is at large and escaped justice. You or I find him, are 100% sure it's him, and know that he did it. Maybe he admits it to our face to help. Any way about it we have a handgun conveniently in reach. The decision: do we go Batman style and drag him into the courts (at risk of escape) or shoot him and be done with it?
Now I'm no gun slayer, I don't even play games of that nature, but I can tell you which I 
wish I would do. There'd be a terrible psychological block to killing someone, but I believe I'd do it.
Am I taking revenge? Yes. I am serving justice. By all Biblical standards he is to die, and if I don't kill him he might try it again, maybe even on me. Self-defense is in.
Slightly more close example to Inigo Montoya: A man has sworn to kill my whole family. Maybe he's already got my dad. Again, he isn't looking and I found a handgun that's pre-loaded. Whatta we do?
A little harder to choose, but choose we must. Who's it gonna be, him or me? Self-defense.
At the risk of being irreverent, God says "I will repay" and He might just choose to do it by having me find that gun in either of those cases.
Now let's consider our beloved comic hero Inigo Montoya. The six-fingered man killed his father. Justice will never reach him other than by the hand of our favorite Spaniard. Maybe justice must come by Inigo's hand.
What? All that talk for a maybe? For me it's a maybe, still clouded. But hopefully all my talking points have brought you far enough to decide. Is Inigo doing right? Then tell it that way. Is he not? Then he's doing wrong, and glorifying wrong cannot be right.
Interestingly though, we live in a post-Christ era. Do we believe that he really will mete out vengeance? He says he will. And if he will then I'm okay with leaving him to do that, if even selfishly because he'll get 'em ever worse than I could.
So I am Inigo. The six-fingered man is asleep and I have my hand-gun. I can take his life or leave it.
Sleep peacefully, villain. My name is Reiyen, you're the man that killed my father... and one day if you don't get it right my Father's gonna kill you and good. I don't need to bring that day any closer.
So where am I in regards to the question asked? I think that even Inigo falls under the negative portrayal section (although I love that movie and especially his role *is conflicted*). Really, it's comedy. It's not meant to be real. So I put it under the exceptions to the rule that Neil mentioned.
Other exceptions:
1. If you have restructured some of the morals of your world. (In my world, the deity figure is not quite omnipotent, which could change things).
2. All the self-defense type revenge actions I listed above.
3. As an act of war. Ehud assassinated the king of Moab. Samson pulled down the temple on the Philistines. And in my world, the race of men has it in for the demon lords because of the evil they has done. They're in perpetual war.
4. When it isn't really vengeance, but protecting others from real threats.
5. Others... enjoy finding and discussing them 

(well, Airi, when you find this thread... this is my version of a monster post? How'd I do?)