We’re looking for software that facilitates preparing charts, graphs, etc. for the layout/graphic design process. Something with MS Excel’s ability to take a data set and transform it into a graph. However, instead of Excel’s analytical engine, we’re looking for something that gives much more control over the visual aspects of the final product. That is, it doesn’t need to crunch any formulas per se, just generate high quality vector art, with all the control over movement, colour, etc. that you have with Illustrator. Illustrator has rudimentary graphing capabilities, but they are far from sufficient when working with a data-heavy report. For example, they can generate a graph from data, but cannot automatically display data labels (even though the underlying data is there). Excel has good graphing functionality, but lacks the high-end control of design elements necessary for professional print publication.
To clarify a little bit, we’re looking for software geared more towards the graphic design market than the analytical/business market. Somewhat like the difference between Word and InDesign/Quark. You can write papers and publish with both, but InDesign has a strong focus on control over placement and appearance of individual elements. You don’t (generally) publish books with Word, and you (generally) don’t write your dissertation in InDesign.
ticker is right. I use R for exactly what you described in your post. The graphics are very, very customizable. If you can imagine what you want to do with your graphs, R can make it happen because of its fine graphics control. It outputs to the vector formats that ticker mentioned in addition to the other usual formats.