Are you talking about when you gain reputation in the dialogue box or where? Typically Red font indicates a loss of reputation, Green or Black Font represent a gain in reputation. There are some oddities in the text colors due to the game expanding over the years.
Do you notice a title associted with the Reputation level such as Hero, Friendly, Known, Rascal, Bandit, Arch-Enemy?
Reputation scores in green tend to mean you will get a more positive reaction from those places, Reputation scores in black tend to be neutral, and reputation scores in red will get aggressive response. Exactly how that impacts game play, quests, etc varies.