Assuming you mean viewing files in their list view (as opposed to icon view), then the colours are taken straight from your palette. Changing them without changing the palette (and as a consequence everything else) is a bit fiddly. You could always try a workbench replacement like Magellan or Scalos, however.
At least this issue is addressed in OS4.x, which allows rather more customisation of the list view. Pity you can't turn off the small icon preview in the lister - one reason I use list views in the first place is for speed and that seems to slow it down slightly.
