Warp plasma appears to burn green. (Obvious observation is obvious.)
For example, in the Star Trek Voyager episode Fair Trade, weapons fire ignites a cloud of warp plasma that had been seeping out of a container with disabled safeties. The subsequent explosion is a rather intense green:
(Yes, that's a person on fire, but it's OK - he's a drug dealer)
In an earlier Voyager episode, Investigations:
"Neelix manages to gain the upper hand and Jonas is knocked over the railing into the plasma-stream from a ruptured plasma conduit, incinerating him instantly." (Memory Alpha)
I am unsure if the plasma had been ignited or was just leaking.
In the real world, copper burns green, as does chromium and krypton gas is used in green neon signs.
Why does warp plasma burn green? Is there a (pseudo-)scientific reason, or is it just part of the story? Does it burn this color in other Star Trek series?
Answer
I asked about plasma being able to ignite and burn at all over on Physics.se. The answer is the same as Kevin's comment. Plasma is composed of free electrons and nuclei, and can't ignite or burn in the traditional chemical sense. There are tests being done with nuclear reactions to ignite plasma, but nothing conclusive yet.
However, because warp plasma is fictional, it has fictional properties and I suspect it burns green because green gas in special effects suggests it is very unhealthy for the victims and because our eyes can see green very well compared to some other colors, the brightness of the 'flame' seems brighter through the TV than if it were another color.
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