I think you might want to take a look at the following two:
Gnuplot is a portable command-line driven graphing utility for linux, OS/2, MS Windows, OSX, VMS, and many other platforms
It's probably the number one graphing tool for scientific data (at least where I come from). Here's a list of demos. You sometimes have to prepare the data for it in a rather awkward way, but it's very widely used.
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS
This is the one I prefer for graphing, as it plays nicely with data of any kind, although it can be used for much more than that. There are some graphics here.
Both of them have those features:
- they are fully scriptable
- they are free
- they run on all platforms
- you can customize every last inch of the graph
It does however take some time to get used to either of them and you'd definitely need to read the documentation, but your wishes are all fulfilled.
The nice thing is that you can have the application not only output images in a GUI, but you can also script them to update output automatically to a folder.