• Abinit - an open source robust plane wave density functional code
• Wien2k - Electronic structure calculations using density functional theory based on a full-potential linearized augmented plane wave approach.
• LM Suite - Linear Muffin Tin Orbital package that support full potential and atomic sphere approximation (ASA) calculations.  It can also model electronic transport in nanoscale structures using a non-equilibrium Green's function approach.
• PARSEC - (Pseudopotential Algorithms for Real Space Energy Calculations) solves density functional calculations using a real space approach.  This technique is ideal for modeling small clusters.
• PHONOPY - Phonon calculations at harmonic and quasi-harmonic levels.
• CPMD - Car-Parrinello Molecular Dynamics - This code can be used to perform ab-initio molecular dynamics calculations.  It allows for time-dependent density functional calculations, wavefunction optimization, and path-integral molecular dynamics.
• Siesta - (Spanish Initiative for Electronic Simulations with Thousands of Atoms).  This code using numerically truncated orbitals (single and double zeta approach) to build an order-N density functional code.  This code is ideal for modeling large scale nanostructures (i.e. nanotubes, nanowires, molecules).
• Plato - (Package for Linear-combination of ATomic Orbitals) is a suite of programs designed and written by Andrew Horsfield and Steven Kenny. Capabilities of the program include a tight-binding algorithm, and a self-consistent field method using either a local density approximation or generalized gradent approximation functionals. The program was specifically developed for application to systems with periodic boundary conditions (crystals), however it is also possible to treat isolated molecules. PLATO was written with speed of calculation as a priority, and uses numerical basis sets and tables of pre-computed one- and two-centered overlap integrals.
• Quantum Espresso - (also known as PWscf)  This plane wave density functional code takes advantage of ultra-soft pseudopotentials to accelerate calculations.  In addition, it has the ability to handle magnetic structures, calculate phonon dispersions, and perform structural relaxations.
• Fleur - This code is based on the all-electron full potential linear augmented plane wave approach.  It can provide important check for plane wave calculations and also has special options for handling surfaces and 1d structures.
• QuantumWise (formerly Atomistix) ATK and VNL - This commercial package provides the ability to calculate I-V curves in nanostructures and molecular junctions.  The code is based on a non-equilibrium Green's function approach and it also takes advantage of numerically truncated orbitals to allow for calculations of large systems.
• Gaussian - This quantum chemistry package comes with a wide range of features, including the ability to predict optical spectra, NMR spectra, and reaction pathways.
• Akai KKR - This code uses a multiple scattering approach to determine the electronic structure of materials and nanostructures.  One unique feature is the ability to model the electronic and magnetic properties of alloys through the use of the coherent potential approximation (CPA).
• VASP (user license required) - this widely used plane wave density functional code can be used to simulate a wide range of material properties.

 Molecular Dynamics/Empirical Potentials

• LAMMPS - general purpose molecular dynamics simulator that has the option to use leonard jones potentials, embedded atom potentials, and potentials for biomolecules and proteins.  This parallel code can easily handle systems with thousands of atoms.  The ability to incorporate the effect of temperature provides an important complement to density functional techniques.
• DL_POLY - DL_POLY is a parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith and T.R. Forester under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Molecular Simulation Group (MSG) at Daresbury Laboratory.  You can find a local tutorial on DL_POLY here and this code was also discussed at the 2007 CNF Fall Workshop.
• GROMACS - this molecular dynamics code was designed primarily to examine biochemical molecules such as proteins, lipids, and nucleic acids.  It can also be used to simulate proteins.  The authors have done considerable work on optimizing the code.
• GULP - The General Lattice Utility Program can be used the simulate the elastic and phonon properties for 1D, 2D, and 3D materials using a large library of empirical potentials.

 Nanophotonics

• MPB - MIT Photonic Bands package.  This code can calculate the band structure and electromagnetic modes of periodic dielectric structures.
  
• MEEP - This is an open source finite difference time domain (FDTD) simulation code that was developed at MIT.
• MULTEL - This code models the acoustic and phonon transport through multilayers and phononic crystals.
• DDSCAT - This code uses the discrete dipole approximation to calculate the scattering properties of nanoparticles at a range of wavelengths, polarizations, and mediums.  The code can be used to tailor the plasmonic response of nanoparticles.

 Nanoscale Electrostatics

• UTQUANT - This is a quasi-static CV simulator for one dimensional silicon MOS structures.
• SEMC-2D - Schrodinger Equation Monte Carlo 2D simulator for quantum transport and inelastic scattering effects in nanoscale semiconductor devices such as nanoscale double gate MOSFETs and tunnel injection lasers.   A dissertation providing more details on the approach is available here.

 Multiscale Physics 

• Elmer - This multiphysics packages allows you to model coupled problems.  This could include current induced heating, vibrations in cantilevers, and fluid flow in microchannels.