I used an older (~ 2yr) version of sigma in a case where D3 couldn't hack it. There were 10's of thousands of nodes, and D3's approach of SVG elements were not as efficient as the sigma.js canvas approach. my needs were minimal though, so none of the extra d3 features came into play (and this was also before sigma had plugins).

to lay out the graph i was running dot from graphviz on the server. took too long client-side.

I'd say D3 is a super set of the features in SigmaJS. D3 is more comprehensive in the sense that there are so many types of visualizations you can make using just D3.