I think for use flags:
red = use flag was and is still enabled
blue = use flag was and is still disabled
yellow = use flag will change with this emerge, also shows percent sign for a cue without colors if I remember
For the package status flags on the left, the color coding is pretty obvious and I believe just corresponds to the letters it's showing (N = new, R = reinstall same version, U = upgrade version, S = slotted package, B = package blocking occurred, etc)