PumpLinx now includes the capability of modeling free surface problems with its multiphase module using the VOF (volume of fluid) method.
Fuel tank sloshing, self priming pumps, and other gas/liquid scenarios can be simulated accurately within hours.
Here is a link to a video http://youtu.be/-V_PYjkntiQ demonstrating a number of scenarios run in PumpLinx, including: gear box sloshing, flow over a weir, breaking of a dam, fuel tank sloshing, and a self priming pump.
PumpLinx is the 3D transient CFD software for pumps, compressors, turbines and valves by Simerics.