Modifier genes act WITH another gene.
In mice, the easiest colour-or-pattern one I can think of is "umbrous" - most Self Black mice and Black Tan mice carry it, but it does not show on their coats. However, if you have an Agouti mouse (the agouti ticked-hair pattern is dominant to 'self-coloured' hair and an agouti is a black mouse with ticked hairs) the Umbrous modifier causes most of the black ticking to appear 'darker' on the top side of the mouse. An Agouti mouse without 'umbrous' will usually have even ticking all over -and the 'strength' of the umbrous gene (or group of genes) can determine the level of effect.
A quick search on Google also revealed that there are a number of "mouse modifier genes" that have to do with health and susceptibility to disease.