Staffanstrops,
To change the color of the selection you would set the fillsymbol or the linesymbol of the popup.
//initialize popup window
var popup = new esri.dijit.Popup({
fillSymbol: new esri.symbol.SimpleFillSymbol(esri.symbol.SimpleFillSymbol.STYLE_SOLID, new esri.symbol.SimpleLineSymbol(esri.symbol.SimpleLineSymbol.STYLE_SOLID, new dojo.Color([255,0,0]), 2), new dojo.Color([255,255,0,0.25]))
}, dojo.create("div"));
You can also find out how to disable the selection in the popup documentation.
Here is the documentation reference:
popup-amd | API Reference | ArcGIS API for JavaScript