It is my understanding that, generally speaking, the main colors in the Marseilles are the three primary colors: Red, blue and yellow. Red is supposed to signify solar/male qualities, and blue lunar/female. Note that these are qualities, and not literally sun men and moon women. Yellow is supposed to symbolize the "purity of incorruptible gold". Also in the deck is the pink fleshy color, signifying what is human and related to humanity. Green isn't nearly as important, but is supposed to signify resurrection. White - secrets and initiation. And finally, violet - moderation (as far as I can tell this is only supposed to be in the Temperance card, if it's there at all).
I got all of this from a dictionary of symbols that discusses colors along with the other symbols in each card, using the Marseilles deck as its basis.
I myself also use the Universal Marseilles deck, and have also wondered how accurate its colors are. As far as I can tell, they're not perfect, but they're generally pretty close. Taking into consideration the color scheme of the entire card, combined with the card's meaning without regard to color, I think it's fairly easy to guess what is original and what has been altered. The only major changes that really bother me is the change in coloration of the hair of the Hanged Man and the Star: it's supposed to be blue.