There are tremendous resources for d3 visualization techniques. Here we focus on force layout with collision detection as an under explored medium.
bostock
This clustered force layout is implemented using two custom forces. The first, cluster, pushes nodes towards the largest node of the same color. A second collide force prevents circles from overlapping by detecting collisions. An exploration in three parts. blocks 
cunningham
We developed
this idea for drawing factory locations on a map where clustering
of the factories physical locations made no traditional map scale or
projection suitable. We approximated the effect of a wall map filled
with push-pins by placing dots as close to the proper map location
as possible without overlapping neighboring dots. blocks
We applied the same technique to visualize the progress of
concurrent webserver transactions. Transaction progress will slow under load.
Our dots slow proportionally and collide with more neighbors.
The visual effect shows general contention without suggesting
more meaning than that congestion and slowness can correlate.
blocks