Apply multiple prefabs at once. Select all your prefabs and use either shortcut or Tools menu item to apply and revert. (You can change shortcuts in the script if you want, currently it uses ctrl+shft+a to apply and ctrl+shft+r to revert)

ApplySelectedPrefabs.cs

// Credit: baptisteLar from http://forum.unity3d.com/threads/little-script-apply-and-revert-several-prefab-at-once.295311/
public class ApplySelectedPrefabs : EditorWindow
{
    public delegate void ApplyOrRevert(GameObject _goCurrentGo, Object _ObjPrefabParent, ReplacePrefabOptions _eReplaceOptions);
    [MenuItem ("Tools/Apply all selected prefabs %#a")]
    static void ApplyPrefabs()
    {
        SearchPrefabConnections (ApplyToSelectedPrefabs);
    }

    [MenuItem ("Tools/Revert all selected prefabs %#r")]
    static void ResetPrefabs()
    {
        SearchPrefabConnections (RevertToSelectedPrefabs);
    }

    //Look for connections
    static void SearchPrefabConnections(ApplyOrRevert _applyOrRevert)
    {
        GameObject[] tSelection = Selection.gameObjects;

        if (tSelection.Length > 0)
        {
            GameObject goPrefabRoot;
            GameObject goParent;
            GameObject goCur;
            bool bTopHierarchyFound;
            int iCount=0;
            PrefabType prefabType;
            bool bCanApply;
            //Iterate through all the selected gameobjects
            foreach(GameObject go in tSelection)
            {
                prefabType = PrefabUtility.GetPrefabType(go);
                //Is the selected gameobject a prefab?
                if(prefabType == PrefabType.PrefabInstance || prefabType == PrefabType.DisconnectedPrefabInstance)
                {
                    //Prefab Root;
                    goPrefabRoot = ((GameObject)PrefabUtility.GetPrefabParent(go)).transform.root.gameObject;
                    goCur = go;
                    bTopHierarchyFound = false;
                    bCanApply = true;
                    //We go up in the hierarchy to apply the root of the go to the prefab
                    while(goCur.transform.parent != null && !bTopHierarchyFound)
                    {  
                        //Are we still in the same prefab?
                        if (PrefabUtility.GetPrefabParent(goCur.transform.parent.gameObject) != null && (goPrefabRoot == ((GameObject)PrefabUtility.GetPrefabParent(goCur.transform.parent.gameObject)).transform.root.gameObject)) 
                        {
                            goCur = goCur.transform.parent.gameObject;
                        } 
                        else 
                        {
                            //The gameobject parent is another prefab, we stop here
                            bTopHierarchyFound = true;
                            if(goPrefabRoot !=  ((GameObject)PrefabUtility.GetPrefabParent(goCur)))
                            {
                                //Gameobject is part of another prefab
                                bCanApply = false;
                            }
                        }
                    }

                    if(_applyOrRevert != null && bCanApply)
                    {
                        iCount++;
                        _applyOrRevert(goCur, PrefabUtility.GetPrefabParent(goCur),ReplacePrefabOptions.ConnectToPrefab);
                    }
                }
            }
            Debug.Log(iCount + " prefab" + (iCount>1 ? "s" : "") + " updated");
        }
    }

    //Apply      
    static void ApplyToSelectedPrefabs(GameObject _goCurrentGo, Object _ObjPrefabParent, ReplacePrefabOptions _eReplaceOptions)
    {
        PrefabUtility.ReplacePrefab(_goCurrentGo, _ObjPrefabParent,_eReplaceOptions);
    }

    //Revert
    static void RevertToSelectedPrefabs(GameObject _goCurrentGo, Object _ObjPrefabParent, ReplacePrefabOptions _eReplaceOptions)
    {
        PrefabUtility.ReconnectToLastPrefab(_goCurrentGo);
        PrefabUtility.RevertPrefabInstance(_goCurrentGo);
    }
}