Well there's a lot of different configurations out there, on most new capcom machines it's an arrangment of red, green, and blue, and on the older machines it was an arrangment of red, white, and blue. I say go with whatever colors suite your control panel, some of the cooler combinations I've seen are:
1-player 2-player
pp, bu, gr yl, or, rd
pp, bu, gr yl, or, rd
Yeah yeah, it's basically a rainbow, no gay pride jokes intended, but the gradient look gave the control panel an awesome feel.
On my control panel I made one-player blue, and two-player red, and it turned out pretty good. A major factor in the look though is the control panel, so if you have ilke white buttons on a black control panel, their gonna stand out, but if you have black buttons on a black background, it's gonna blend in so well they're gonna be impossible to see. So before you buy all your parts, I suggest maybe A: drawing it out and coloring it to see what looks the best to you, or B: if you can't draw, just cut out construction paper on a cardboard box, seriously, I made all my prototypes out of cardboard, works like a charm and you can throw it away afterwards, no fuss.
-CthulhuLuke