In the original Star Wars trilogy, we see only a very limited number of lightsabers. Luke and Ben's are Blue. Vader's is Red, and later, Luke's is Green. They're all cool, primary colors (RGB). The whole contrast of Luke's Green vs. Vader's Red (diametrically opposed colors) is nice and symbolic and all. And yet, when I first started my RPG campaign, I never once thought that lightsaber colors would be limited to these three. In my campaign, we had different shades of blue and green, one purple saber and even a nice golden blade for the Tusken jedi. It just seemed to make sense to me that such things would exist—plus it was a nice differentiator to make Jedi just a bit more unique.
When the prequel trilogies came out we first saw much the same: Green and Blue for the good guys, Red for the bad. But there WERE anomalies (Windu's purple blade) that seemed to support the theory of multi-colored sabers. Yes, the bulk of the Jedi seemed to use either blue or green (witness the battle of Geonosis), but there was never anything explicitly stated that ruled out other colors.
And then, somewhere in the Expanded Universe, someone had to make up a rule that there were no longer any other colors but red, blue and green. This went on further to make lightsaber crystals exceedingly rare and that the 'source' (singular) of other colored crystals was lost/destroyed long ago.
This bothers me on several levels. First of all...why even come up with this needlessly restrictive 'rule'? It doesn't make sense. Its a huge galaxy and you're telling me there is only ONE source for non-blue-green lightsaber crystals? If they were this rare, it would stand to reason that the blue-green crystals would also be so, and if they WERE why hadn't the Sith destroyed these few sources as well (they had 20 years to do so under Palpatine). Bleh. To me, it just seemed like another lame author running with what he thought was a 'cool' way to tie in something he saw in the prequels and make a plot point out of it. But to me, it just doesn't make sense.
In the Knights of the Old Republic games, there are various different crystal colors (gold and purple in the first game, and lots of different variations in the second)—and I see no reason why that should have changed. As I said before, its a fun and harmless way in the RPG for people to personalize their Jedi and make them a bit more visually unique. Symbolically, I think this goes hand in hand with the diversity of races represented in the Jedi Order, too.
KotOR also introduced the idea of lightsaber color relating to jedi 'specialty'. I don't entirely buy into this as a hard, fast rule, but I did find it interesting. Blue for Guardians, Green for Counselors and Gold for Sentinels (spys). I can see where that might be something of a tradition, but I'd never limit my players to that.