If you’re on a mac, iWork ‘09 make some incredibly nice looking charts.

Academic journals tend to care a lot less about the glitziness of the chart and a lot more about the accuracy and precision of the data represented in the chart.

@cwilbur is right. When I make graphs for publications, I do them in excel. I use a program called jmp for my data analysis, and the charts that come out of that program are terrible, so I export the statistics that jmp has created for me and then recreate the graph using excel.

Others in my lab use statistica, which is a great statistics program and can make publishable graphs, but I unfortunately learned on jmp and haven’t had time to relearn statistics programs. If you’re looking for something to do analyses with as well, that’s a very good program.

Of course this all depends on the kinds of charts you want to be making… Anything specific?

If you’re on Mac, “plot”—http://www.apple.com/downloads/macosx/math_science/plot.html is one of the best I’ve found.

Excel makes great charts if you know how to really work it.

However, I use SPSS to make most of my charts simply because I generally use SPSS to analyze data.

It’s hard to beat Excel.

@J0E: Actually, if you’re looking to make a box plot, it’s a piece of cake. Excel doesn’t offer that feature.