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Software libraries for scientific data processing and visualization require you to write computer programs to access their interface and facilities. For simple tasks, this might sound over kill. For complicated or routine works, it might be a good idea to invest some time initially, developing a processing/visualization program with the help of software libraries listed here.
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Libraries   ([CM] Commercial, [SR] Shareware, [GPL] GPL)

AVS/Express [CM] -- help build applications for interactive, multi-D visualization and graphics.
biggles [GPL] -- a Python module which help create publication-quality 2D scientific plots.
BLT -- Tk extension with plotting widgets of X-Y graph, barchart, stripchart.
Cgraph -- ANSI C library for generating PostScript scientific plots.
DISLIN -- high level library that displays data as plots, charts, contours and maps.

DISGCL -- an interpreter language based on plotting library DISLIN.
DrawP3D -- a scientific visualization subroutine library with parallel operation via PVM.
EDA ---a collection of FORTRAN subroutines for exploratory data analysis.
FLEXIO -- an API for storing multi-D scientific data.
FXDR -- call XDR routines from Fortran and make binary data IO portable.
GDChart -- high performance library for creating charts and graphs in GIF format.
Gnudl [GPL] -- high-level language for manipulation and plotting of data.
NEW Grapher Library -- a C++ library for writing OO code to create scientific graphics.
Graphite -- creation of scientific, engineering, and business graphs with Python.
GtkPlot [GPL] -- Gtk widget for drawing high quality 2D scientific plots.
Gri [GPL] -- programming language for drawing science-style graphs.
HDF -- a library and data format for the storage and exchange of scientific data.
HDF5 -- completely rewrite of the HDF portable binary format and supporting library.
Histo-Scope Plotting Widget Set -- six Motif widgets for graphing and plotting.
HOPS -- processing data in netCDF files conforming to NCAR-CCM or NCAR Ocean Model format.
IEEEIO -- a compact library for storing multi-D scientific data in portable binary format.
Infomap [GPL] -- a Java component for displaying and manipulating nodal data.
ION [CM] -- efficient data analysis/visualization for Web client applications.
Java 2D Graph Package [GPL] -- a package of Java classes for scientific data plotting.
NEW KavaChart [CM] -- collection of Java applets/beans/libraries and imaging tools for data visualization.
Khoros Pro 2000 SDK [CM] -- development tools for data analysis/visualization, visual programming, GUI, client/server software.
LATS -- a library to output gridded data in support of some intercomparison projects.
Libgraph [GPL] -- library to provide generic graph building capabilities.
NetCDF -- an interface and software library for scientific data access.
MexCDF -- allows MATLAB users to read, write, and manipulate NetCDF data files.
Ncview -- a visual browser for netCDF format files.
NetCDFPerl -- perl extension module for scientific data access via NetCDF.
OpenViz [CM] -- for business professionals to visualize/interact with growing volumes of data.
PACCO -- an object-based approach to data processing by extending Tcl/Tk.
PGPLOT -- Fortran 77 subroutine package for scientific 2 plots.
pgperl -- provides an interface for the Perl language to the PGPLOT.
ptcl -- provides an interface for Tcl to the PGPLOT.
STAP -- interactive graphics and data analysis program based on PGPLOT.
WIP -- simple to use interface designed to produce high quality graphical output based on PGPLOT.
PLplot [GPL] -- scientific graphics library with C/C++ or Fortran interface.
PSPLOT -- Fortran-callable PostScript 2D plotting library,
Ptplot -- a Java plotter based on xgraph.
Qplot [CM] -- C graphics library that allows you to draw easy color plots.
ROOT -- an object oriented framework for large scale data analysis.
SciPlot [GPL] -- a widget capable of plotting cartesian or polar graphs.
SDTS++ -- a C++ toolkit for SDTS files.
TAL -- an Eiffel OO library for technical analysis applications.
View3D [CM] -- OSF/Motif compliant widget for creating 3D data displays.
VisAD -- a Java class library for visualization/analysis of numerical data.
VuSystem -- programming system for dynamic manipulation of temporally sensitive data.

Also Check Out:
aiSee -- calculates a customizable layout of graphs specified in GDL.
CAM C++ Class Libraries -- graphics, matrix/vector and symbolic function classes.
ClibPDF -- ANSI C library for direct PDF generation.
Grafix [GPL] -- C++-package for assisting programmers to write programs with GUI for X Windows.
KPlotW/KPlot [GPL] -- a plotting widget and an interface to it.
NEW Matpack [GPL] -- a C++ numerics and graphics library.
plotutils [GPL] -- plotting of scientific data and the drawing of vector graphics.
StudioJ [CM] -- integrated Java components for data analysis/charting/database access.
UfMulti -- a distributed data analysis toolkit.
XMove [CM] -- a software engineering tool for visualization tasks.

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