Sometimes we get requirement to change the text colour for some fields in Dynamics CRM 2013 in order to highlight them in different colour. I wrote one for text field but recently got asked to change for Lookup field in a query. I do suggest that it is unsupported, but still as an experiment here it goes:
You can add the scripts on-load or based on some condition.
For changing colour during field is non-selected:
//Setting red colour
Now Lookup Field looks like this:
Note: This is unsupported script and may break in future if Microsoft changes something.
Hope it helps!