I'm fascinated by both d3 and Raphael. I understand that Raphael is built on top of D3 and that it is cross-browser compatible, but I'm not sure which one is better suited for what scenarios. Can somebody please shed some light? My immediate use-case is potentially using the SIMILE timeline and integrating it with a state diagram (for which I intend to use d3/Raphael). Thanks!
Raphael is not built on D3.
Raphael will help you draw elements. D3 is more comprehensive and will help you bind data to elements. So I'd say D3 is more powerful. This forum discussion Discusses presenting a SIMILE timeline using D3, they refer to this project which implements a timeline in D3. So at first glance, D3 is your answer.
However, given that there doesn't seem to be a widget for D3 which handles the SIMILE timeline for you, either Raphael or D3 could be a good choice. That is, except for the fact that D3 doesn't work well with internet explorer's earlier versions, as explained in this article. So if you need to support earlier versions of IE, you're better off with Raphael.