Recently, I had to process and plot a significant amount of data. Previously, I used to use gnuplot for that, but I've discovered two shortcomings: 1) gnuplot has limited data manipulation facilities, so I had to do data processing with perl scripts, 2) it has very arcane syntax and it's rather hard to make it do what you want, especially when you have slightly complex requirements (eg. bar charts of several nested data sets).
I have resisted learning R for a long time, because it also uses a rather arcane language with many complex and rather badly documented data structures. However, a week ago, I remembered my last experience with gnuplot, and I gave R a try. I'm glad I did even though it took me some time to get used to its data manipulation capabilities since the learning curve is rather steep. However, once you get used to it, it's so much easier and faster to manipulate data than with custom-made scripts, and much simpler to produce well-looking plots. Visit its homepage and take a look.