Typically, morality is found in either the intentions (did you mean to do good?), the consequences (were the results good?), or in the act itself (even if it is done with good intentions and to achieve a good end, you could say taking a life is still evil). I think you knew that, though.
Or, to shoot myself in the foot, you could go with something like good is, "maximize the happiness of the most people, even if that group doesn't include yourself." Then evil is maximizing unhappiness. You could define morality by relativism - it makes me feel good, so it is good. Or go the other way and invoke the divine - "god says it is evil, so it is."
The long and short is that there are many definitions of good and evil, as well as right and wrong, and the two pairs are not even necessarily the same (though some do believe they always are). Additionally, much of what we would classify as good/evil/right/wrong is completely ingrained through culture, religion, upbringing, and experience. I could point out some extreme examples, but that
would be derailing the thread.
[Lasso] Needless to say, V's actions fall strongly into the evil category for me. For example - if Kubota was outlining his plan, who's to say they couldn't have been foiled? Whose to say Kubota's trial even would have gone as he said? The Paladins
can detect evil, after all; maybe Kubota isn't evil at all. Who is to say his rule over the Azure Fleet (for lack of better term) would be any better or worse than Hinjo? There are too many variables for it to be entirely Neutral; V killed a person not out of good motives, but selfish ones.
Of course, let's ask another question - does V's alignment even matter?
And we can muddy up your precious "intent," as well. Once you get into the psychology of it all, how do you know for sure what you intended? There's always subconscious desires, battles between the id, ego, and superego, and so on. Think that's a load of fecal matter? Well, so do I about chaos theory wrecking ethical consequentialism.
Or for that matter, who says you have a choice? If your personality, dictated by your genes and environment, are a consequence of causality, then whose to say your "decisions" are actually choices? Maybe that's all been predetermined. However, I think I fall in StreamOfTheSky's camp - that infinite causality (ie, your action has effect beyond your scope to comprehend) is a convenient excuse to engage in rampant relativism.
Of course, all that said - it's these themes that make a story interesting. Would this comic be more interesting or less if V was clearly in the right or wrong? My guess would be the latter.