N-Body/Particle Simulation Methods
An extensive online tutorial with examples and code references.
http://www.amara.com/papers/nbody.html

NEMO
[open source - Unix] An extendible stellar dynamics toolbox; has various programs to create, integrate, analyze and visualize N-body and SPH-like systems. In addition there are various tools to operate on images, tables and orbits, including FITS files to export/import to/from other astronomical data reduction packages.
http://bima.astro.umd.edu/nemo/

CFD codes list
A large list of commercial, public-domain and shareware Computational Fluid Dynamics codes.
http://icemcfd.com/cfd/CFD_codes.html

Aarseth's N-body software
[open source - multiplatform] Direct N-body algorithms.
http://www.ast.cam.ac.uk/~sverre/

Hut Treecode Algorithm
[open source - multiplatform] A guide to a tree code algorithm implementation, used for astronomical N-body simulations.
http://www.ifa.hawaii.edu/~barnes/software.html

Stellar Astrophysics Software
[open source - Windows] Various programs for stellar astrophysics. Includes CHANDRA stellar structure software for collapsed objects including rotating white dwarfs and neutron stars, and STARCAL for nuclear astrophysics and the stellar structure of main sequence stars with supernova forecasting.
http://grnwd.tripod.com/thelostchord.html

Laboratory for Computational Astrophysics
A joint project of the National Center for Supercomputer Applications and the Department of Astronomy of the University of Illinois.
http://zeus.ncsa.uiuc.edu:8080/lca_home_page.html

COSMICS
Cosmological initial conditions and microwave anisotropy codes for cosmological modelling. COSMICS is a package of fortran-77 programs.
http://arcturus.mit.edu/cosmics/

CAPGADGET
[open source - multiplatform] Visualization package to capture and display Gadget N-body simulations.
http://www.geocities.com/capgadget

ORSA - Orbit Reconstruction, Simulation and Analysis
ORSA is a C++ framework for the development of algorithms and programs oriented to the simulation and analysis of the orbital evolution of bodies in space.
http://orsa.sourceforge.net