What plotting / visualization tools are useful in generating good plots?
I guess Python has great tools for this, especially IPython Notebook: http://ipython.org/notebook.html . It has good visualization opportunities and at the same time you could document your code and make it re-configurable and online. Of course it best for visualizing data low dimensions and creative visualization algorithms can be prepared either in OpenGL or high level languages such as MATLAB.

In 3D, if appropriate, time varying surfaces can be embedded in 2D and shown as a 3D volume. For generic 4D visualizations you could either use videos, or accumulated volume maps. For visualization of high dimensional data, always make sure you check methods such as Multi Dimensional Scaling.