I just got my car recently (96 Civic Coupe VTi) and the people that sold it to me said that the red key if used in the ignition will render the black keys useless -.-

I then called up Honda to ask how much a replacement black key would be, as long as I had the red key it would cost $82.50 for a replacement key, then an additional $60 to get it cut and reprogrammed, would take about 2 hours. If I didn't have the red key then they have to order it by serial number or something.
I didn't actually need an extra key as I still have both- but the rubber is coming off and I thought if a new key wasn't too expensive I would get a sexy new key... Guess I have to live with the ugly ones for now...

(Off topic: I also asked how much seat covers would cost, $1100 pure lambswool!!!)