We did not use any pre-existing JS plotting library.  At the time we were exploring our options (and I believe this still to be the case), the plotting libraries were all architected to (1) have their plots specified by JS code, (2) interact with mouse/keyboard via DOM events and JS callbacks; (3) process data locally in the JS namespace.  Flot was one of the few that actually had any support for callbacks to retrieve data from a server, but even so, its data model was very limited.

We recognized that in order to support good interaction with a non-browser language, we would need a JS runtime that was *designed* to sync its object models with server-side state, which could then be produced and modified by other languages.  (Python is the first language for Bokeh, of course, but other languages should be pretty straightforward.)  We also wanted to structure the interaction model at a higher level, and offer the configuration of interactions from a non-JS language.

It's not entirely obvious from our current set of initial examples, but if you use the "output_server()" mode of bokeh, and you grab the Plot object via curplot(), you can modify graphical and data attributes of the plot, and *they are reflected in realtime in the browser*.  This is independent of whether your plot is in an output cell of an IPython notebook, or embedded in some HTML page you wrote - the BokehJS library powering those plots are watching for server-side model updates automagically.

Lastly, most of the JS plotting libraries that we saw took a very traditional perspective on information visualization, i.e. they treat it as mostly as a rendering task.  So, you pass in some configuration and it rasters some pixels on a backend or outputs some SVG.  None of the ones I looked at used a scene-graph approach to info viz.  Even the venerable d3.js did not do this; it is a scripting layer over DOM (including SVG), and its core concepts are the primitives of the underlying drawing system, and not ones appropriate to the infovis task.  (Only recently did they add an "axis" object, and there still is not any reification of coordinate spaces and such AFAIK.)

The charting libraries that build on top of d3 (e.g. nvd3 and d3-chart) exist for a reason... but they mostly just use d3 as a fancy SVG rendering layer.  And, once again, they live purely in Javascript, leaving server-side data and state management as an exercise to the scientist/analyst.

FWIW, I have CCed the Bokeh discussion list, which is perhaps a more appropriate list for further discussion on this topic.  :-)

-Peter