Sort children by name in selected gameobjects. Unity3D 4.5+ (C#).

TempTools.cs

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

public class TempTools {
  
	[MenuItem ("AShim/SortChildrenByName")]
	
	public static void SortChildrenByName() {
		foreach (GameObject obj in Selection.gameObjects) {
			List<Transform> children = new List<Transform>();
			for (int i = obj.transform.childCount - 1; i >= 0; i--) {
				Transform child = obj.transform.GetChild(i);
				children.Add(child);
				child.parent = null;
			}
			children.Sort((Transform t1, Transform t2) => { return t1.name.CompareTo(t2.name); });
			foreach (Transform child in children) {
				child.parent = obj.transform;
			}
		}
	} // SortChildrenByName()
	
} // class TempTools

Method to sort all the children inside another children

using UnityEngine;
using UnityEditor;
using System.Collections.Generic;
using System.Linq;

public static class SortChildren
{
    [MenuItem("Setup/Sort All Children")]
    public static void SortAllChildren()
    {
        foreach (Transform t in Selection.transforms)
        {
            SortChildrenRecursively(t);
        }
    }

    public static void SortChildrenRecursively(Transform parent)
    {
        List<Transform> children = parent.Cast<Transform>().ToList();
        children.Sort((Transform t1, Transform t2) => { return t1.name.CompareTo(t2.name); });
        for (int i = 0; i < children.Count; ++i)
        {
            Undo.SetTransformParent(children[i], children[i].parent, "Sort Children");
            children[i].SetSiblingIndex(i);
        }
        
        foreach (Transform child in parent)
        {
            SortChildrenRecursively(child);
        }
    }
}