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Have you seen this? http://www.advsofteng.com/

I was looking for graphing and charting stuff last year. The only thing I found at the time was ChartDirector. There have been a couple of other open source ones posted above that I may investigate in future, but finding this was what I needed at the time.

Ploticus is a versatile, free program, although more for presentation and business graphics than scientific plots.

ChartDirector is commercial software but it's cheap and the free version is a complete implimentation with an inobtrusive watermark.

VPython does some neat tricks, mostly 3D, but some 2D as well:
http://vpython.org/

ChartDirector produces snazzy looking charts, but Edward Tufte proably would not care for them:
http://www.advsofteng.com/

If you don't mind dropping $99, ChartDirector is pretty good. Good documentation, lots of features, good support, responsive to bug reports. It runs on Windows, Linux and FreeBSD.

You need chart director. I use it for various web-based charting, and it's much faster than ms charts.