aiSee automatically calculates a customizable layout of graphs specified in GDL (Graph Description Language). This layout is then displayed, and can be interactively explored, printed, and exported to various formats.
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.
P. Heim, J. Ziegler, and S. Lohmann. Proceedings of the International Workshop on Interacting with Multimedia Content in the Social Semantic Web (IMC-SSW 2008), volume 417 of CEUR Workshop Proceedings, page 49--58. Aachen, (2008)
P. Chapman, G. Stapleton, J. Howse, and I. Oliver. 2011 IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC), page 87-94. (September 2011)
P. Heim, J. Ziegler, and S. Lohmann. Proceedings of the International Workshop on Interacting with Multimedia Content in the Social Semantic Web (IMC-SSW 2008), volume 417 of CEUR Workshop Proceedings, page 49--58. Aachen, (2008)
S. Kuznetsov, and S. Obiedkov. Principles of Data Mining and Knowledge Discovery, page 289--300. Berlin, Heidelberg, Springer Berlin Heidelberg, (2001)