I haven't found a single anime that has come close in terms of its use of strategy, deduction, and justice as general thematic elements throughout the plot. In fact, I'm still searching for an anime that is similarly good. I know a lot of people suggest Code Geass, but it's not quite the same for me.
The use of Light as both a protagonist and antagonist at the same time always served as an interesting principle as well. Of course, while at the end he is almost entirely a villain, you can still see shades of his righteousness.
I think if I'd have to break it down, it's because Deathnote focused on just a few thought-provoking principles, but did them very well, is why it's so great.
