Personally, I really like gnuplot. There are other ideas in the nodes below.

• Portable simple line graph module?
• Charting Modules
• Professional, "a-la-OpenOffice", 3D graphs
• develop animation and graphics
• creating graphs
• (YA) Q: re "which graphics module?"
• How to print/draw a network graph
• Real time data graphs.

I'm also looking at SVG for a project of mine (An SVG Case Study: Integrated, Dynamic Avalanche Forecasting has some nice examples).