I'm not sure if this is more a AOTC or EU thread, so I'll drop it here.
I know the question of why so many lightsabers seemed to change color (like Mace's going from blue to purple, Ki-Adi's going from purple to blue, etc) before AOTC has come up several times.
Of course, from a film point of view, the good guys are all blue and green (except Mace, whose purple definitel means something), and bad guys are all red. I'd imagine this is in large part to make it easier to see onscreen who's who.
We know from previous EU sources that lightsabers are primarily built from adegan crystals, which focus the light into the "blade" and determine its color. We also know from the AOTC Visual Dictionary that Mace's standing on the council allows him to have the gold-plated hilt (but, I believe, says nothing about the color), and that Sith use red blades due to the artificial (slightly unstable) adegan crystals they use.
Since no one with any official say seems to have addressed the sudden shift from all colors of the rainbow (pre-AOTC) to the standard four (AOTC - ROTJ), and back again (post-ROTJ), here are my thoughts. Until I'm told they're wrong, I'll believe this explanation:
Various natural factors cause crystals from different planets to produce different color blades.
Prior to the turmoil surrounding the Battle of Naboo, lightsabers were a show of individuality among the Jedi. Although the most readily-available crystals produced blue and green blades, it was not uncommon for higher-ranking Jedi to seek out crystals from other planets so that they could have lightsabers with blades in nearly any color imaginable (including a red similar to that produced by the artificial crystals used by the Sith). Although the green and blue sabers generally lasted longer, many Jedi preferred the different colors.
Following the Council's realization that the Sith had returned, expeditions to less conveniently located worlds simply to obtain crystals of a different color were seen as frivolous and strongly discouraged. As worlds ceded from the Republic to join the Confederacy, crystals native to these worlds were absolutely unavailable to use. Consequently, as lightsabers were destroyed or simply wore out, they were replaced by crystals producing green or blue blades. Mace Windu was the last of the Jedi to take part in the Battle of Geonosis to have a differently-colored blade, as his was more recent in construction and still in proper working order.
Then came the Purge. For many years, the only known functioning lightsabers were those belonging to Anakin Skywalker and Obi-Wan Kenobi. (It's possible that Qui-Gon's also survived, though wasn't used.)
Some time after constructing a simple green-bladed saber, Luke Skywalker found evidence of varying blade colors and encouraged his students to use whatever crystals were available. As political climates on many planets had changed, the full spectrum was again available.
Corran Horn built a dual-phase saber with adegan crystals (producing a green blade) and a diamond (producing a white blade). However, diamonds typically produce weaker, less stable blades, so they were rarely used except as a last resort, even though they were readily available throughout the Clone Wars.