D3 still seems to be the best of the bunch: most mature and most flexible. Right now we're using a combination of R for heavy data processing and refinement, and D3 for visualization. They make a good pair.
Interestingly enough almost all my coding has been in the browser since I've been using Tributary [http://tributary.io/] for D3 prototyping and RStudio Server for R (which is amazing if you haven't tried it)
Although I haven't used it yet, it's worth mentioning Shiny from the RStudio team http://www.rstudio.com/shiny/ which makes it pretty painless (so I hear) to create interactive R visualizations.
2 I could get over, I suppose, but I really need something slick, simple & fast that works in IE.
Raphael.js is really just a nice way to handle svg, and so it lacks some of the niceties of d3 as far directly tying your visualization to the data. But it's still a great tool.
I've seen that some people tried combination of d3.js and Raphael in order to overcome this issue (for instance: http://stackoverflow.com/questions/9559365/raphael-and-d3-js...), but I haven't tried it myself yet. I would be very interested to hear any experiences regarding this particular combination (d3, raphael).