Nanoscale physics tools
Density Functional Theory (DFT) calculations
abinit Feature-full package for electronic structure calculations.
etsf-io I/O library for the platform-independent exchange of electronic structure data.
libxc Comprehensive library of exchange-correlation functionals.
openmx Package for nano-scale material simulations.
See also DebianScience/Chemistry.
http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_software has a list of software - both free and commercial.
gdis A GTK based program for the display and manipulation of isolated molecules and periodic systems.
v-sim V_Sim visualizes atomic structures such as crystals, grain boundaries and so on
Scanning probe microscopy
gwyddion Scanning Probe Microscopy visualization and analysis
XAS/ XAFS / EXAFS
horae (contrib) interactive graphical processing and analysis of EXAFS data.
ifeffit (contrib) An interactive program for XAFS analysis
sixpack (contrib) full-featured package for XAS analysis
objcryst-fox A program for the ab initio structure determination from powder diffraction.
pymca Python toolkit and application for X-ray fluorescence analysis.
fityk Fityk is a flexible and portable program for nonlinear fitting of analytical functions (especially peak-shaped) to data (usually experimental data). In other words, for nonlinear peak separation and analysis.
Numerical Computation (MATLAB/IDL like)
http://blends.alioth.debian.org/science/tasks/numericalcomputation lists Matlab/IDL like packages for calculations on arrays, data analysis and visualisation.
Computer Algebra Systems
See DebianScience/ComputerAlgebraSystems for a comparison of some of these.
maxima Maxima is a fully symbolic computation program.
yacas Yacas is a small and highly flexible computer algebra language.The syntax is very close to Mathematica. The distribution contains a small library of mathematical functions, but its real strength is in the language in which you can easily write your own symbolic manipulation algorithms. It supports arbitrary precision arithmetic.
See http://blends.alioth.debian.org/science/tasks/imageanalysis.html for applications to extract quantitative data from images.
Tools with unofficial .deb
cmpr peak fitting and x-ray diffraction data viewer already packaged by Carlo Segre
expgui GUI for GSAS (OK for Debian but GSAS isn't) already packaged by Carlo Segre
mcmaille x-ray structure solution already packaged by Carlo Segre
tpf x-ray profile refinement already packaged by Carlo Segre
xgen macromolecular crystallography already packaged by Carlo Segre
Gxsm Gnome X scanning microscopy package, tool for data acquisition of STM/SPM/AFM and visualization, available from http://gxsm.sf.net.