Alignment is a clumsy attempt at an ethical system. The old Law/Neutral/Chaos system copied Moorcock without really understanding. Adding a Good/Evil axis only made the problem worse: it devolves quickly into "horse opera" morality: the white hats are Good no matter whom they kill, and the black hats are Evil no matter their real motivations. Even Tolkien, inventor of endless cannon fodder, regretted defining an entire race as irredeemably evil.
D&D 4th Edition made a step in the right direction by divorcing alignment from mechanics, and defaulting to "unaligned" unless a character truly plays hero or villain. Yes, in some stories only the Pure of Heart can find the Grail or wield the Ultimate Weapon, and Darkest Evil is a palpable force, but that should be a DM's decision based on behavior. (Admittedly, mechanisms from World of Darkness or Pendragon might help quantify Good or Evil).
"On two occasions I have been asked [by members of Parliament], 'Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?' I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question."
- Charles Babbage (1791 - 1871)