Frank Losasso’s PhD thesis on fluid simulation, which contains previously unpublished work on coupling together SPH and level set based fluid simulations:
Algorithms for Increasing the Efficiency and Fidelity of Fluid Simulation
Eftychios Sifakis’ PhD thesis on face, muscle, speech, and surgery simulation:
Algorithmic Aspects of the Simulation and Control of Computer Generated Human Anatomy Models
Geoffrey Irving’s PhD thesis on a variety of physics simulation topics:
Methods for the Physically-Based Simulation of Solids and Fluids
Update: While I’m doing the thesis thing, here’s a couple slightly older ones that are probably worth a look.
Adam Bargteil’s PhD thesis on liquid surface tracking.
Surface Tracking and Texturing
Bart Adams PhD thesis on point-based graphics:
Point-Based Modeling, Animation and Rendering of Dynamic Objects