(ArcGIS API for JavaScript) Sample of adding popupTemplate to a mapservice layer in 3.x.

Sample.js

require(["esri/map",
         "esri/layers/ArcGISDynamicMapServiceLayer",
         "esri/tasks/query",
         "esri/tasks/QueryTask",
         "esri/dijit/Popup",
         "dojo/dom-construct",
         "esri/dijit/PopupTemplate",
    "dojo/domReady!"
], function (Map, ArcGISDynamicMapServiceLayer,Query, QueryTask, Popup, domCon, PopupTemplate) {

    var map = new Map("map", {
        center: [-118, 34.5],
        zoom: 5,
        basemap: "topo"
    });
  
  var layer = new ArcGISDynamicMapServiceLayer('http://sampleserver6.arcgisonline.com/arcgis/rest/services/USA/MapServer');
  map.addLayer(layer);
  
  var myQuery = new Query();
  myQuery.where = "1=1";
  myQuery.outFields = ['*'];
  
  map.on("click", function(e){
    console.log(e);
    myQuery.geometry = e.mapPoint;
    var queryTask = new QueryTask("http://sampleserver6.arcgisonline.com/arcgis/rest/services/USA/MapServer/2");
    queryTask.execute(myQuery, function(result){
      console.log(result);
      var popupTemplate = new PopupTemplate({
        title: "My popup",
        fieldInfos: [
            { fieldName: "state_name", visible: true, label: "State Name: " },
            { fieldName: "pop2000", visible: true, label: "Population: " }
          ]
      });
      
   
      result.features.forEach(function(f) {
        f.setInfoTemplate(popupTemplate);
      });
      
      map.infoWindow.setFeatures(result.features);
      map.infoWindow.show(e.screenPoint, map.getInfoWindowAnchor(e.screenPoint));
      
    });
    
  });
  
  
});