cmXT: Glad you like it. =] I don't think I've ever drawn Mugen outside of tiny, squiggly doodles before, so it was a fun contrast compared to Jin and his typical blank expression (which is what makes their interaction in the anime so great, ya?).
Dacon: My process is rather... haphazard. But yeah, I definitely adjust my colors according to the environment and lighting conditions that I want for the piece. Though that usually doesn't come to me when I first choose my colors... instead, I let Photoshop do all the heavy lifting.
I use a lot of adjustment layers to try get the color scheme I want, which I mostly picked up from doing tags/random graphics.
Usually it goes like this...
1) Put down flats/basic shading (usually just attached shadows, with the flat color serving as the highlight) - this is just eyeballing the colors, everything on separate layers, neutral gray background. Obviously, you have to have some inkling of where the overall lighting is to do so, but if you don't have an unusual light source in mind from the start, just go with the tried and true overhead one.
2) Change background color to whatever "atmosphere" I want - this is where I can sort of establish the overall color scheme of the piece.
3) Use a color balance and/or hue/saturation adjustment layer on the fills to make it fit the environment/bg color (usually by making them either warmer or cooler depending). Most of the time I end up turning saturation down since most lighting environments aren't strong enough to make things too bright.
3b) If I royally screwed up on a certain color choice in step 1, I can always go back and adjust the individual layer.
4) Add reflected light from the environment.
5) ???
6) profit!
For example, after doing step 1... I just applied different adjustments to get different lighting conditions and environmental feels. This is just initial groundwork for a piece though - if I were to develop any of these, there are further adjustments to be made (eg toning down the contrast between skin tone and clothing in the night time one), but it's definitely not a half-bad way to try to find an overall look.