Turbulence.2D, from Jawset Visual Computing, brings fluid dynamics to After Effects, with 7 channels of video input, one texture coordinate channel, and numerous other controls to help create organic textures, animations and typographic effects. You can find samples in their gallery, more about features, and a demo version at Jawset.
A similar filter in public alpha testing from the same company was mentioned last year in AE smoke filter(s) in alpha.
Update: BTW, there was similar filter Fluid Dynamics filter from Electrocolor that was released for AE 7.0/CS3. And Kevin Goldsmith noted that David Lenaerts has created a smoke/fluids simulation in Pixel Bender utilizing 49 Pixel Bender kernels per frame; he's giving out the source code.