The force graph has been the subject of my fascination in the recent couple weeks. One of the fun things about the force layout is that the positioning of each node and link is calculated at every tick, which means the normal update-transition paradigm doesn't work too well.
This was my approach to the enter-update-exit pattern in a force graph, and other then a couple bounces of the nodes, seem to work pretty decently.
Modified http://d3js.org/d3.v3.min.js to a secure url
Modified http://underscorejs.org/underscore-min.js to a secure url
https://d3js.org/d3.v3.min.js
https://underscorejs.org/underscore-min.js