With the removal of alignment restrictions during the early months of 2012, color crystals in Star Wars: The Old Republic have pretty much lost any "traditional" meaning they may have once had. In the good old days, the bad guys had red and the good guys had blue or green, just like in the movies. There have always been oddball colors - orange, yellow, purple, and the black-core variants of all the other colors - but the three primary colors of light remain the Force-user standards. Jedi use blue and green, Sith use red.
There is, of course, some historical basis for this. In the first two movies (Episodes IV and V), the good guys had blue lightsabers and the bad guy had a red one. The reason for this is simple enough - those colors showed well on the screen, and made the combatants easy to distinguish during the lightsaber battles. Obi Wan's instant force-ghostification came at the swing of an evil red blade, and that was all you really needed to know about that. Bad guys use evil red stuff, always.
Two old men slug it out during simpler times
When Episode VI: Return of the Jedi came along, things changed. Technology had advanced since the 1970s and the rotoscoped lightsaber blades looked even better on-screen. But in the sarlaac pit rescue scene, Luke had to fight a bunch of guys against the rich blue of a desert sky - a blue blade would not show up well against the Tatooine backdrop. So they decided to make the blade of his newly-crafted lightsaber green. The number of lightsaber blade colors was increased by 50% because skies are blue (and Lucas hadn't yet perfected ballsy revisionism enough yet to go back and change the colors of the previous two films).
Red and green lights and a family brawl - just like Christmas!
That's the technical reason for the green sabers, anyway. According to non-canon sources, including SWTOR lore, blade color is determined by the color (and quality) of the crystal used in the weapon's construction, and often reflects the wielder's role. Historically, blue indicated Jedi Guardian, green indicated Consular, and yellow indicated Sentinel. The red crystals favored by the Sith are artificially created in laboratories, and somehow imbued with Dark Side energy, which makes them universally red. Color crystals are almost purely the invention of non-canon Expanded Universe writers and game designers. In canon material, crystals are mentioned only once in the novelization of A New Hope as an embedded decoration a lightsaber's hilt. It is only in the Expanded Universe that blade color is assigned any kind of meaning.
Flash forward to the 1990s. Digital filmmaking revolutionized special effects. Live action characters are more or less seamlessly combined with cartoony CGI characters, for good or for ill. For Episode I, Lucas stayed with the three primary blade colors and added some Hong Kong-style wire-fu to make the fights more awesome and dynamic. Qui Gonn used a green blade, Obi Wan used blue and Darth Maul used red. The two Jedi used different colored blades so we could tell them apart, and the bad guy, as usual, used his vile red blade.
Ganked by two Jedi from the same guild. Welcome to Huttball.
Mace Windu's amethyst-bladed saber in Episode II is the only non-primary-color blade that appears in the movies. During the massive Jedi-vs-droid arena battle, all the lightsabers in evidence are blue or green. Count Dooku uses his fancy red-bladed saber, and Yoda's saber is revealed to be green. Mace Windu's lightsaber was made purple, totally unique in all six films, not because it had any kind of meaning, but because Samuel L. Jackson requested it, and Lucas agreed to the request. Because when Sam Jackson asks you for something, you just don't say no. According to the Expanded Universe, the purple color reflects his standing as head of the Jedi Council.
Ezekiel 25:17, but with more purple.
So in terms of film canon, there are 4 colors of lightsaber crystal: blue, green and a single purple for Jedi, and red for Sith. The further one branches out from the films, though, the more blade colors one encounters. The first canonical black-core saber blade pops up in the Clone Wars animated series in the form of the "Darksaber." Revan went through a bunch of different colors - purple, blue, red, back to blue, green, and back to purple again. The Expanded Universe books assert that, at one time or another, lightsabers came in every color of the rainbow. Which brings us to SWTOR's color selection.
Blue, green and red are still the most commonly-encountered sub-50 lightsaber colors in SWTOR. You can find these things everywhere, and there are all sorts of Artifice crafting recipes for them at all levels. Orange and yellow are the next-most common - orange crystals are found in a lot of mid-game custom weapons, and yellow crystals can be crafted fairly easily. Purple and magenta are next, most commonly encountered at level 50 - there are level 50 magenta crystal schematics available from vendors, and purple crystals come standard with some endgame weapons. Black-core sabers are fairly rare, but you'll see a few tricked-out 50's with black-red, black-blue, black-green, black-orange and black-purple blades. The black-green crystal available during the Rakghoul plague event made that color fairly prominent for a while, and the white crystal that was available for a little while from the time-limited crystal vendor on fleet is arguably the rarest.
It can also be used to scan hotel rooms for trace bodily fluids.
In terms of stats, there is no real difference between one color and the next at the same level. At level 50, they are all +41 to one stat, and there is no difference between a red +41 Endurance crystal and a blue +41 Endurance crystal, except for the color. It's really all about the look, and what you want to say with your character. Currently, I have two level 50 lightsaber-wielders - a Sith Sorcerer and a Sith Juggernaut. The colors I picked for them have rather specific, personal meanings to me, and were chosen well before the characters hit 50.
The Sorcerer has the black-green level 50 Endurance crystal from the Rakghoul event. For him, the lightsaber is more or less just a stat stick - he doesn't really use it much for fighting, but will occasionally take a whack at enemies when he runs out of power. I picked up the black-green crystal fairly early in his career and held onto it for level 50. I liked it because it looked poisonous, and that reflects his personality and his combat style.
He doesn't get to swing it much, but it makes him look venomous.
The Juggernaut has a purple Endurance crystal. I got that one from the limited-time crystal vendor that was stationed on Imperial Fleet until Patch 1.2 went live. It cost 150,000 credits, and I sort of regretted buying it. Since the crystals are pretty much just for looks, and I was going for the classic Darth Vader look, I was tempted to stick with a traditional red crystal. But when I look at him now, and compare the look of a red blade with that of the purple blade, somehow the purple blade looks more sinister. For whatever reason, the black-purple crystals don't look as scary as the bright purple blade he carries now.
For some reason, the purple blade looks scarier than a red one.
My lower-level Sith Pureblood Jedi Sentinel is using whatever he has at his disposal - currently a green and a yellow crystal he made himself - but I may switch him to an orange crystal later on. For now, it suits him to maintain the ruse that he is following the path of Light, but he is struggling against his Sith nature and turning dark and vicious. Eventually, he will no longer be able to keep up the act, and his corruption will spread to his weapons. That's my justification for it, anyway. I just think it will look cool to have a Sith Jedi running around with a matched pair of orange-bladed lightsabers. Alternately, I would consider a black-core crystal to reflect the character's inner corruption... but it will be a long while before he can use one of those.
Playing nice... for now.
For my low-level human Sage, who is going full-on Light Side and looks kinda like Jesus, I am using a yellow crystal he made for himself. The golden glow of his blade seems somehow the most Christ-like of the crystals available to him, like he took a halo, bent it straight and uses it to wail on evil-doers. I think he will continue using yellow crystals throughout his career.
Personally, I don't have a lot of interest in the color of my ranged characters' blaster bolts. I have seen characters using black-green crystals in their blasters, and the effect is kind of interesting, but the bolts don't last very long. A lightsaber blade gets a lot of screen time, whipping around in savage arcs, but a blaster bolt is nearly instantaneous. You don't get a lot of time to appreciate how cool it looks, so my ranged guys don't really care so much about what colors they are shooting. It's all about the stats for them - the Powertech uses an Endurance crystal, and the Operative uses a Critical crystal.
So what's in your saber? What color are you using, and why? Let us know in our comments!