I run a small information visualization shop and we use Protovis & D3 exclusively for visualizations on the web.
Bostock's work is the most useful and thoughtful visualization framework on any platform, and at this point the only reason I use Hadley Wickam's ggplot2 is for graphics that need more marks than Chrome can handle on the DOM.
Initially I didn't see what D3 offered over Protovis, but I've since come around---D3 code is closer to the underlying page elements that make up the visualization, so you can leverage your existing HTML/SVG and CSS knowledge. Also, unlike Protovis, D3 has animation baked in by creating/removing DOM elements and tweening their positions and sizes.
The latest public-facing work we did using D3 is this linked treemap & linechart, which uses both HTML elements (treemap divs) and SVG elements (linechart lines):