Calculation
Mathematica Unequalled platform for symbolic and numerical mathematics. A theorist’s best software friend.
COMSOL Powerful, easy-to-use platform for finite-element solution of PDEs. GUI for drawing problem geometry; automatic mesh generation; menu-driven specification of equations, boundary conditions, and parameters; versatile visualization of results.
Simulation
GROMACS Fast, free atomistic MD simulation platform. Well-documented set of command line simulation and analysis tools that work seamlessly together.
Avogadro Well-designed free point-and-click molecule builder and visualizer.
iBabel Converts molecular structure files between the many formats used by various simulation and calculation packages.
Programming
C++ reference pages Excellent online reference for C/C++ language and standard libraries, particularly including the C++ STL (Standard Template Library) containers and methods.
Numerical Recipes in C online Free online version of older edition of Numerical Recipes book.
Python Powerful, well designed, widely used scripting language. An excellent tutorial is here.
SmartSVN GUI for subversion, version control software for collaborative development of programs and documents.
Cyberduck Well-designed, convenient, free FTP client.
Writing
LaTeX By far the best choice for technical word processing. WYGIBTWYT (“wiggib-tawitt”) — What You Get Is Better Than What You Type. Some tutorial and reference sites here:
Cambridge University Engineering Department – Text Processing using LaTeX
TeXLive Open source installation of TeX, LaTeX, TeXShop, BibDesk, LaTeXit.
BibDesk GUI for editing and managing .bib files.
LatexIt GUI for using LaTeX to typeset equations to paste into Keynote, Pages, (Powerpoint, Word,…)
Graphics
GraphicConverter Converts graphics among many formats, as well as performing many editing functions.
GraphClick Indispensable for grabbing data point values from images of graphs.
OmniGraffle Excellent vector drawing program.
Plot Very nice open source 2D plotting program for publication quality plots.
Power Photos Allows you to have multiple iPhoto libraries, easily switching between them.
Searching and reference
Papers Indispensable. Like iTunes for .pdfs; stores journal articles with identifying metadata. Create folders (like playlists) of papers for projects without making copies. Export reference lists as BibTeX files.
Skim A .pdf reader with annotation capabilities — highlight, draw boxes, make notes.
The Cat Penn State library master catalog.
Illiad Penn State portal or ordering copies of papers not available online, requesting interlibrary loans, etc.
NIST WebBook Collection of physical property databases (thermodynamics, transport, spectroscopy).
DIPPR student database Thermodynamics and transport data on *selected* compounds.