Like Mike said, the "transparent" colors that are used in a lot of the show bike / show car special effects jobs (pearls, candies, etc...) , are typically done with urethanes, with all the usual caveats about toxicity and safety.
That said, some of the rc car modelling guys are talking about using the water-based Parma "Fasescent" line of paints to good effect. I've not yet got my hands on these, but just might have to do so to see if there is a good, safer alternative to urethanes for getting these sorts of special effects.
As for ghost flames, the more subtle and "ghostly" the flames are, the more they rely on paint transparency. I've seen other ghost flame jobs that could've probably been done with more opaque paints, just laid on with a very light touch.