Camp Cody
This site has a LOT of information. I think they do a good job of chunking out the content so it's manageable for different users.
Visual Design
Optimal Living Salem
Disclosure: I did this site. But it's one of my favorites.
SPENT
Interactive poverty simulation.
The Global Goals
Institute for Wetland and Waterfowl Research: Ducks Unlimited
Check out the ducks move as you scroll down!
Mapping Nuclear Verification
Kick My Habits. How Much Could You Save?
An interactive "game" that shows savings from avoiding habits like smoking and eating out.
Jinsha River Basin
Column and Veil
As a website, this is a little annoying (you have to click on all the items before you can proceed). But there are some good ideas for learning design.