Another catchup post:
Fluid Simulation with Articulated Bodies from gatech has some nice results, would could make a great basis for a new version of Karl Sims swimmers.
Sony has released Field3d, a open file format for volume data, which seems to take a lot of the low level work away from you when working with voxels, it supports slices,etc. as well.
Matthias Müller also has a new publication, Fast and Robust Tracking of Fluid Surfaces which describes how to efficiently generate surface meshes from fluid simulations.I've not read it fully yet, but presumably it is worthwhile.
I also stumbled accross some more open source fluid projects, Fire Dynamics Simulator and Smokeview from NIST which has some good looking fire & smoke simulations of houses burning, etc. and a new project nsproj, that has a parallel 3D Navier Stokes solver.