Lucas says something to that extent in on of the special features for the AotC DVD. He basically says something like Jedi use blue/gree, Sith use red. Maybe it's like the old cliche of the bad guy wearing black; if a guy pulls out a red lightsaber you know he's a baddie. After that, Sam Jackson asks, "What about purple?" or something like that, to which Lucas replies, "We'll see," or something. So I don't think it's really set in stone.
As stated above, some of the novels like the Jedi Academy Trilogy give more details. Jedi construct lightsabers that are individualized. That however, seems to contradict AotC where everyone's using blue and green. I think maybe though, the lightsaber a Jedi constructs is ceremonial, and part of the padawan training. Perhaps the Jedi also have a stockpile of more generic green/blue lightsabers for battle. For example, in Clones, the Jedi toss Obi-Wan and Anakin lightsabers during their rescue. I doubt these were the characters' actual lightsabers, since Dooku would have almost certainly confiscated Obi-Wan's, and of course Anakin's was trashed in the droid factory.