Nathan Yau of FlowingData has published an up-to-date list of what he uses to turn raw data into his impressive visualizations.
What’s always striking about the tools he uses is that there’s no “quick fix”. He utilizes a range of industry standard data manipulation (e.g. R) and graphic design (e.g. Adobe Illustrator) tools in his work.
I particularly liked his comments on processing and formatting data
Assuming I have the data I want (big assumption), this is a stage of tedium. Solutions typically reflect my state of I-want-this-to-be-done-already, and I use whatever tool is closest. I would use a hammer if I could.