I’ve been gathering papers on realtime weather simulation, and one of the best attempts at cloud simulation appears to be that of Mark Harris’s PhD Thesis and further work from 2002 onwards. Harris, M Realtime Cloud Rendering for Games.
His method involves understanding the thermodynamics of clouds as well as utilising methods to realistically render them, using such issues as scattering and absorption of light. He also describes using 2D imposters to speed up the rendering. However, general home computing power may have improved enough since 2002 to enable a mix of full-particle based clouds, with the use of imposters only for distant clouds, or indeed, the rendering of a skybox.