Doesn't just a flame model with a single shader works? I've never tried it before (I've used brushes and textures when I needed a flame) but it could look cool ingame.
What I mean is instead of like, an image sequence of an animated fire, it would be a fire with the vertices fading to red then finally black, and the actual shader itself could be a tcMod scroll upward with an rgbGen vertex. Maybe it could also look cool with a GT128 thrown in there as well for an alpha fade, so we get sharp fires where it fades. It would still be single stage and also work in vertex light mode, as well as being a method compatible with the PCX2 and ATI Rage.
Fire is only an example from this. It could also be applied to smoke, rays, maybe even muzzleflashes