I've gone and picked 2 for each color, and tried to keep it to a maximum of 2 from any single game as well. Feel free to ignore the second one listed for each color if you think this is too many noms.
BlackMario (Super Mario RPG): Mario's hair color has oscillated between black and brown depending on the artist and the game, but it's unquestionably black in SMRPG.
Tharja (FE13): Ohohohoho.
BrownDelita Hyral (FFT): Something I've always noticed about FFT character art is that the nobles are almost universally blond while the lowborn are almost universally brown-haired. The game never really makes a point of it, but I wonder if it was intentional.
Yosuke Hanamura (Persona 4): Have some support, brown-hair team.
BlondPrincess Toadstool (Super Mario RPG): Because this team needed more support.
Jerin (Lufia 1): No, really, it did.
RedEliwood (FE7): At least he's not Roy, I suppose.
Mitsuru Kirijo (Persona 3): This team actually DOES need more support.
SilverCecil Harvey (FF4): This is a slightly debatable color: his sprites have purpleish hair, but his portraits and his Dissidia design are more decidedly silver, so I classified him here. Anyway, Micaiah will appreciate Cover.
Setzer Gabbiani (FF6): Another debatable one, it's either platinum blond or silver. The sprite favors the latter, though.
Blue:
Lucina (FE13): Because I can't nom Marth.
Naoto Shirogane (Persona 4): Because she's cool, dammit.
TealEirika (FE8), Ephraim (FE8): Fuck yeah brother-sister duo of awesome.
PurpleLiza (SaGa Frontier): You'd be surprised how hard it is to come up with purple-haired PCs.
Ilyana (FE9/10):
Super
PinkNoa (Legend of Legaia): Pink is also surprisingly hard to come up with characters for in the ranked list.
Presea Combatir (Tales of Symphonia): See above.
GreenSelan (Lufia 2): Selan's hair color is kind of ambiguous. It's undebatably teal in her Lufia 1 appearance, kind of a pastel green in her Lufia 2 walk sprite, undebatably green in her L2 menu and battle sprites, undebatably *blue* in her L2 official artwork, and finally undebatably teal again in the L2 remake. In any case the ranked form of her is the one with all the green. So it goes.
Shaymin (Pokemon DPP): Well, the leafy "fur" on its back is most definitely green. I'm of the opinion this is close enough to count, and who says all the noms here have to be human?
As an aside, SF, I think Lucca's pink, not purple (feel free to correct me, though). Also, Liete is G1, not G2, Djinn >_>