At my startup (https://www.novus.com/) we've built a financial data viz product using Protovis and D3. Once we've gotten over the initial hurdle of needing to support IE (we don't anymore), SVG graphs are the bomb. They print beautifully and offer virtually endless customization options. If you can code it, you can draw it. Expect easy interop with tools such as jQuery (which makes our graphs interactive) and Tipsy. The latter we use to provide tool tips that show underlying numbers that have gone into drawing any particular graph.
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):
I'm not a Javascript expert and I don't know D3 so I may be missing something here. I'm trying to add a d3 matcher for http://underthesite.com/, referenced in a contemporary thread:
It fails to detect that http://keminglabs.com/ukuni/ uses d3. What's missing from the matcher? I notice that there's no script tag for d3 in the ukuni main page source.
I am actually a bit confused as to why one of my stream graphs is floating up and to the right. I need to contact support and see where I'm doing this wrong (the two streamgraphs are using the same drawing code, but one has generally more equal proportions of activity across the input values).
I used Protovis for about 6 months and then switched to D3 about 2 months ago. In those 2 months I reimplemented everything that I had built in Protovis, cut down on complexity and lines of code, and have not seen its limitations (and I would consider my use cases extreme).
There have been core design changes to the library that have given it this ability. This page - http://mbostock.github.com/d3/tutorial/protovis.html -demonstrates very well how impressive the author and library is.
