There is really no unified theory/opinion about what the lightsaber colors mean, if anything. So the general consensus among fans seems to be that it's just based on personal preferance of the user (aesthetics) and tradition (the Sith seem to like red a lot).
George Lucas says on the AOTC DVD behind the scenes that "blue and green are for good guys and red is for bad guys."
He doesn't say why, just that it is, so it's not really an "in-universe" explanation.
Define "bad guy" and "good guy." Is Anakin a "good guy" when he slaughters the Tuskens? He's using a blue lightsaber at the time and we never see him use a red one until 23 years later (barring any revelations from Episode 3 of course, but I won't got here for fear of spoilers).
In the same scene on the DVD Samuel L. Jackson asks George if his character can have a purple one. George seems to like the idea and says sure.
So we know it's an artistic choice by the people behind Star Wars, but what does it mean in-universe? Again, no consensus. I've read plenty of conflicting reports.
The theories like the "master padawan" thing don't really hold true, and the "Unified Force" (blue) vs. "Living Force" (green) and "Sith/Dark Side" (red) theory is very good, but unfortunately AOTC seems to fly in the face of it, by introducing Purple and having characters switch colors mid-battle (does that mean they switched philosophies for a second?). Likewise even in TPM Obi-Wan uses both "good guy" colors.
I've read (ad naseum) the theory that red sabers are somehow inherently evil. This seems supported by JA's single player, because your saber suddenly turns red when you go to the Dark Side, even though you had no time to build a new one. But, these theories are based on the idea that the Force of the user decides the color (which begs the question of what color a non Force users's saber would be, such as Han, Aurra Sing, or any other character that has wielded one). If a "good guy" grabbed a Sith Lord's lightsaber and used it against him, would the blade change color suddenly?
Likewise the "red is evil" theory often mentions that "Sith use the Dark Side energy through synthetic crystals."
Though according to official material, Luke uses synthetic crystals for his Green lightsaber in ROTJ, and he had no access to anything "Sith" related and he was not (at the time) being tempted by the Dark Side.
So my vote is with personal preference and tradition. Or perhaps it's something else entirely...