This is where most of the money is, and so the biggest and most expensive products are here, too. Most engineering firms that have anything to do with fluid dynamics have at least one piece of CFD software in their toolshed, whether they wrote it themselves, bought the license from a CFD company, or just contract out to specialists. Most government and academic research in CFD involves specialized codes. The commercial codes are not specialized enough to tackle typical research problems.
Academic institutions have their share, too.
Here's a nice list of inexpensive research codes. Since cost and visual impact are higher priorities than realism in CG, non-CFD solutions are typically preferred. Proprietary house codes are relatively rare. Two examples are PDI's water in Antz and ILM's waves in The Perfect Storm. Look for the Advanced Fluid Simulator.