I haven't worked with d3 but was able to put together a jsfiddle with both. With other libraries like this, I usually elect to let Enyo do the main layout and then render the other into an Enyo control. I don't know if this will work for you but here's the code I used.
http://jsfiddle.net/ryanjduffy/PfwNL/1/
function buildGears(node) {
// code taken from http://bl.ocks.org/mbostock/1353700
}
enyo.kind({
name: "ex.App",
kind: "FittableRows",
components: [
{kind:"onyx.Toolbar", components: [
{content: "d3 + EnyoJS"}
]},
{name: "d3", kind:"Scroller", fit:true}
],
rendered: enyo.inherit(function(sup) {
return function() {
sup.apply(this, arguments);
if(this.hasNode()) {
buildGears(this.$.d3.node);
}
};
})
});
new ex.App().renderInto(document.body);