So I've been thinking about some literary character and have been having some trouble putting them in alignment "boxes". Curious what opinions are out there.

Varys (of A Song of Ice And Fire /Game of Thrones) - Spymaster, and manipulator of events. Works for the good of the kingdom, but proves quite morally flexible in methods. -- I've seen him variously categorized between Neutral Good and Chaotic Neutral in listicles around the net.

Edmond Dantes (the Count of Monte Cristo) -- Seeks vengeance/justice for the wrongs done to him, while rewarding those that have found misfortune from keeping their honor. Doesn't seem to be too concerned about potential collateral damage in his schemes. Casually and masterfully manipulates people into their downfall. -- The "righting the scales" aspect of his character would suggest True Neutral; though the vengeful motivations and willingness to let relatively innocent people suffer in the process might suggest more Lawful or Neutral Evil (almost Punisher-esque)?

Sir Percy Blakeney (the Scarlet Pimpernel) -- Master of deception. Uses his talents to rescue people condemned to execution by what he considers an unjust legal system. -- Seems pretty Chaotic Good as he comes off very Robin Hood-esque, except he seeks to help the (formerly) rich rather than the poor.

It's often hard to put alignments to characters since writers are not thinking in terms of alignments. Often stories involve character change, and what has changed can frequently be interpreted as their alignment. So a character who is rigidly obedient to the laws and the "system" might change into one who flouts it (law to chaos), or a character who is neutral might come to take a particular side, such as good or lawful.

I don't remember Varys (I have tried my best to completely block the 3 novels of Ice and Fire that I've read from my mind, because I came to detest that series), but someone who is "morally flexible" cannot be describe as Good or Evil, in my opinion. Moral flexibility implies neutrality.

It's difficult to put people in an alignment category when the results of actions often don't match the intents. (It happens more often than one might expect.) I know of characters with very Good intentions create results usually attributed to very Evil characters. Are the characters good or evil?

Then there's the whole perspective issue: Doing what they think is best for everyone when others have different ideas what's best for everyone.

Then there's the whole interpretation of what is Evil, Good, Lawful, Chaotic, and what sits between all that. Some people consider things that are disparate to be one of those categories depending on the context. Then, there're those who consider there to be more than 2 axes to personalities and the 2-axis method just doesn't work for them.

My view: Don't bother with alignments when unnecessary. When necessary, choose whether to focus on the intent or the results for judgment of alignment (such as when using optional rules of aligned planes). This goes for fictional characters in novels.

In many other settings, outside of D&D, concepts like good and evil can be seen as relative or contextual -- whether something is evil may depend on context or point of view. In D&D, good and evil, law and chaos, are not (traditionally) contextual, but are absolutes. For instance, denizens of the Abyss in D&D are not evil from a "certain point of view" -- they are absolute chaotic evil, and have no redeeming features that could be argued on a contextual or point-of-view basis. 

Any fictional source whose author does not work from the assumption that Law/Chaos/Good/Evil are supernatural and physically real forces, but are instead contextual, will not have characters who behave in accordance with D&D alignment.