The Civilopedia is great, seeing as how I'm not about to remember every characteristic of every terrain feature, unit, civ, etc.
I haven't really read the historical stuff; I really should. I imagine I'd learn a lot of stuff from it, even if it's often best taken with a grain of salt (although life in our day and age typically requires a salt mine, anyway).
Sevopedia and the Unit Upgrade Chart mod are also real assets, even after Firaxis fixed that whole icon fiasco.
Probably the only thing I find that could use improvement/fixing would be the lack of more technical gameplay rules under the concepts listing; it's a bit aggravating when your search for something--perhaps, regarding how a specific part of diplomacy deal-making works--ends up futile.
But yeah, whether it's the Civilopedia from the old DOS game, the one in Call to Power (which even had fictional "historical" entries for all the future stuff), or even the Colonizopedia from (what else?) Colonization, I've always found the feature useful. Heck, I get driven crazy in Master of Magic, since it doesn't have any kind of "Magicalpedia," and I always end up needing/wanting to know something that such a feature would have information on.