Here are some ideas:
Mrrshan = red (blood = warriors)
Darlok = purple (the purple ships are sneaky looking)
Alkari = green (some of the green ships look birdish, kinda like the Amonkrie ships; besides the Alkari diplomat in MOO2 is green)
Humans = blue or white (they always get those colors in sci-fi because they're supposed to be noble or something
)
Psilons = white or blue (same as Humans)
Ithkul = any shipset but with the "choose race" colors (none of the shipsets look like the MOO3 Ithkul ships but they actually don't look evil... now jet black ships with a glow about them...
if you want something more like in MOO2, use the Space Crystal or Guardian palette... or for something really evil, use the "colony" palette!
)
Trilarian - hmm, blue's the obvious choice, but I already used that for Psilon... green's Alkari... I dunno, you figure this out!
Now for some reason the Antaran ship palette seems to be missing... the green one comes close, but not quite
