if you are looking for command line/script driven plotting tools (scientific ;-):
i like gnuplot, it is a very mature program but it is also a little old fashioned/limited (eg.: line style and color can not be changed separately) i have recently discovered gri it feels similar to gnuplot but it is much more flexible and also more intuitive, well at least to me gmt would be something interesting also it is primarily a geograpical ploting tool package but it can do non-geographical representations quit well if you have any need for 3D plots i think this is the best of these 3 programs imre
