Referring to this example:
http://vallandingham.me/stepper_steps.html
it seems that the D3 and jQuery libraries are very similar in the sense that they both do D
Great question!
While both libraries share many of the same features, it seems to me that the greatest difference between jQuery and D3 is the focus.
jQuery is a general purpose library with a focus on being cross-browser and being easy to use.
D3 is focused on data (manipulation and visualisation) and supports only modern browsers. And while it does look like jQuery, it's a lot more difficult to use.