Color Coding Index, Volume 1:
As has been noted, the KMV doesn’t really do that whole ‘good-neutral-evil’ color coding thing. It’s pretty much a faction-based aspect, although IRIS and agents do tend towards white/extremely pale colors and as such is presumably the closest thing to an evil class there is.
Bureau/Central Administration: Blue/black/silver/white. The Bureau itself is pretty variegated because it’s really a Mauveshirt Army at this point rather than a Lawful Stupid Redshirt Army like the rest of the government seems to be (and for much of the timeline isn’t technically military, as such has no standard uniform). Near the end of myth-arc territory, the Administration apparently absorbs it again, thus leading to more standard colors. Despite some variations on him not even remaining a CA agent, pretty much any version of Alexander still uses their colors. Because really, he’s Alexander.
TCS/MRA: Black/silver/grey/white, generally speaking. Due to their lack of any standardized uniform most of the agents have a single color, or set of them, added on (Laura is monochrome+bright blue, for instance). Tobias seems to go in for white/black/gold, which is mostly just an odd variation. Wilhelmina van Helsing was largely red for some reason.
Trevelyans: Alexandra is silver, Morganna is purple, Adrian is blue, Darian is green (and monochromatic, as per above), Serena is blue/medium grey and Julien is red/dark grey.
Crescent Moon Division: Doesn’t generally have a recognizable uniform. Antinomy usually uses either her extremely ominous black/silver long coat or a very srs greenish suit; quite a few of the higher-ups are purple/grey.
Adler’s syndicate: Often black suits with red and white secondaries. Lydia is generally white/brown/red; Kyle takes after her. Their opposition is most commonly brown/blue/silver.
Notable Third Parties: Both Janelle and Lowen, for some reason, seem to go in for white/red/dark brown. Sterling and Mona are green/gold/white and red/gold, respectively. Helena and Xanatov are green/white/black, as is (mostly) the small army under a reasonable approximation of their command. Gale is mostly just black and white, with red and gold as accent colors.
Apart from that, most of the rest of the world just goes with whatever they want to wear that day.