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Berkeley Lab AMR 
Adaptive Mesh Refinement at Berkeley (John Bell and Phil Colella).
Courant Mathematics and Computing Laboratory 
Computational Mathematics and Applied Analysis at Courant Institute (Marsha Berger).
An Adaptive Cell-centered Projection Method for the Incompressible Euler Equations 
Dan Martin's Ph.D Thesis.
Cart3D is a high-fidelity inviscid analysis package for conceptual and preliminary aerodynamic design (Michael Aftosmis).
A C++ library for finite volume simulations. Distributed under the GPL.
Object-Oriented Tools for Solving PDEs in Complex Geometries.
A Free Software (GPL) finite element program.
CFD Resources Online 
Software related to CFD.
Adaptive Mesh Refinement for structured grids 
Very good collection of links.
Science and Fluid Dynamics should have more open sources 
Opinion piece on Open Source and CFD by Stephane Zaleski.
The OpenFOAM (Field Operation and Manipulation) software package can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options.
A Finite Element Differential Equations Analysis Library.
FES2004 tidal atlas 
See also FTP access to data files and source code.
SIMPLE: SIMulation for PLanning the Embolization of intracranial aneurisms
Gerris used to model blood flow in intracranial aneurisms.