Show icon next to items that are prefab root objects.

PrefabStatusHelper.cs

using UnityEngine;
using System.Collections;
using System.Collections.Generic;

#if UNITY_EDITOR
using UnityEditor;

[InitializeOnLoad()]
class PrefabStatusHelper
{
    static PrefabStatusHelper()
    {
        iconPrefabSelf = EditorGUIUtility.ObjectContent(null, typeof(GameObject)).image;
        iconPrefabParent = EditorGUIUtility.ObjectContent(null, typeof(Transform)).image;

        EditorApplication.hierarchyWindowItemOnGUI -= OnHierarchyItem;
        EditorApplication.hierarchyWindowItemOnGUI += OnHierarchyItem;
        EditorApplication.RepaintHierarchyWindow();
    }

    static Texture iconPrefabSelf;
    static Texture iconPrefabParent;
    static GUIStyle prefabTagStyle;

    static void OnHierarchyItem(int instanceID, Rect instanceRect)
    {
        if (prefabTagStyle == null)
        {
            prefabTagStyle = new GUIStyle(GUI.skin.label);
            prefabTagStyle.fontStyle = FontStyle.Italic;
        }

        var obj = EditorUtility.InstanceIDToObject(instanceID);
        var gameObject = obj as GameObject;
        if (!gameObject)
            return;

        var prefabType = PrefabUtility.GetPrefabType(obj);
        if (prefabType == PrefabType.None)
            return;

        var root = PrefabUtility.FindRootGameObjectWithSameParentPrefab(gameObject);
        var prefabParent = PrefabUtility.GetPrefabParent(root);
        var prefabSelf = PrefabUtility.GetPrefabParent(gameObject);
        var prefabObject = PrefabUtility.GetPrefabObject(gameObject);

        var text = (string)null;
        var icon = (Texture)null;
        if (root == gameObject)
        {
            // seems super slow
            //var modifications = PrefabUtility.GetPropertyModifications(prefabSelf);
            //var changed = modifications.Length > 0;

            text = "";
            icon = iconPrefabSelf;
        }

        if (text == null || icon == null)
            return;

        var nameSize = GUI.skin.label.CalcSize(new GUIContent(gameObject.name));
        var textRect = new Rect();
        var iconRect = new Rect();

        iconRect.x = instanceRect.xMin + nameSize.x;
        iconRect.y = instanceRect.yMin + 2;
        iconRect.width = 16;
        iconRect.height = nameSize.y - 1;

        textRect.x = iconRect.x + 18;
        textRect.y = iconRect.y;
        textRect.width = 64;
        textRect.height = iconRect.height;

        GUI.Label(iconRect, icon, GUI.skin.label);
        GUI.Label(textRect, text, prefabTagStyle);

        return;
    }
}

#endif