THEY say that green gets picked up faster by the eye. I use whatever is lying around for fibre but if have to buy replacement I'll go red or green. Doesn't seem to matter to me.
Warm colors (red) advance or draw the eye, whereas cool colors (green) recede, so pick-up time is faster for warm colors. You can test this by letting your eyes unfocus (infinity) and just glance around the room. Notice which colours you see first? It's always going to be the warmest colours that pull the eye.
Problem is the red fibers are not pure red; they tend more towards orange. Adding yellow to red to make orange tends to make it halo slightly or blur the edges somewhat visually. What happens is that for many people they can pick up the red fiber quicker, but can't DEFINE it as quickly when they have to suddenly ratchet down and shoot an accurate shot (on a tight partial for example) so they get better overall results with the green because it doesn't halo as much. Depends a lot on your eyes too, but I found the green didn't really work for me. It was a lot slower to pick up.....for me.
Interestingly, I got pretty reasonable results by just removing the fiber all together and letting natural ambient light shine define the hole in the sight. Great out doors; not so great indoors, but that is the problem with compromise. Some of the green rods actually look more clear than green, so if green is your preference the more desaturated rods would probably work best.
Alternately, if you can ensure that the red/orange fiber is buried flush or slightly below the surface of the front sight so that its edges are surrounded by metal (rather than being pumpkined out over top of it to pick up extra light), the fiber will have better edge definition. This will probably give you the best of both worlds.
Sorry for the excessive nerdiness.