You want to use the colormap function to tell the axes what colors you want to use. That's pretty easy:
colormap([0 0 .5; 0 1 0; 1 1 0; 1 0 0])
But the problem is that MATLAB's colormap lookup is always linear. If your bins aren't all the same width, then it isn't that simple. You'll probably need something like this:
npts = 1e5;
x = randn(npts,1);
y = randn(npts,1);
z = randn(npts,1);
scatter3(x,y,z,32,z,'.')
crange = caxis;
t = linspace(crange(1),crange(2),64);
cmap = zeros(64,3);
mask = t<=.5;
cmap(mask,:) = repmat([.5 0 0],[sum(mask), 1]);
mask = t>.5 & t<=1;
cmap(mask,:) = repmat([0 1 0],[sum(mask), 1]);
mask = t>1 & t<=2
cmap(mask,:) = repmat([1 1 0],[sum(mask), 1]);
mask = t>2;
cmap(mask,:) = repmat([1 0 0],[sum(mask), 1]);
colormap(cmap);
You actually could simplify that a bit because the colormap will clamp to the last color for values that are off the end. That means that you could just have the linspace go between any two fixed values that are convenient. If you do that, you need to pass the values you use into the caxis function so the axes knows the range you're defining the colormap for.
