Well, let me take a stab at it.
I like a bit of history, some context as to what got us to where we are today. That's always a good place to start, I think. Not with "In the beginning..." but with, "Previously, on Dark Heritage..." Hit the ground running, if you know what I mean.
Then I like some simple reference materials. A world-level map, a timeline, perhaps a couple of bullet lists of things like currency and technologies.
I like geographic breakdowns that stay consistent, whether they're national or tribal or whatever divisions. I find geographic organization easier to wrap my brain around than, say, racial or linguistic or historical. That is, I'd rather your broad divisions be "The North", "The Islands of the East" and "The Mountains of Llamaland" (just to stick with the current metaphor) rather than, say, "Speakers of Alpaca" or "50 - 250 Years Ago".
Obviously some things need to be broken out independent of geography but even in, say a timeline, I like to see "50 - 250 Years Ago: In the North," 50 - 250 Years Ago: In The Islands of the East"
On a slight tangent, I don't find that the sorts of organizational systems used in books necessarily translate well to the web. I prefer a richer browsing experience that makes it easy for me to follow my interests around, that rewards me for investigative browsing. My Barsoom site was consciously designed without a very rigourous organizational system so that users would find themselves having to poke around, following links without having a clear guideline as to where they were in relation to the rest of the site.
I know, I know, you're not supposed to do it that way but for some reason, for a campaign setting, it feels right.
I like it, anyway...