To expand Peter's suggestion in the comments ^^:
use scatter3 with cdata parameter cdata :
% generating some sample data [x,y,z]=sphere(50); x=x(:);y=y(:);z=z(:); % the interesting stuff: h=scatter3(x,y,z);
gives you

To add coloring, do the following:
set(h,'cdata',z)
or immediately:
scatter3(x,y,z,'cdata',z);
that leads to

Here the color vector is just the value of z, but it can be anything (as long as it has the same size as x (and y and z).
Gunther struyf
source share