Apply an enchanting glow without actually adding any enchantments.

GlowWithEnchanting.java

package com.comphenix.example;

import java.lang.reflect.Field;

import net.minecraft.server.v1_4_R1.ItemStack;
import net.minecraft.server.v1_4_R1.NBTTagCompound;
import net.minecraft.server.v1_4_R1.NBTTagList;

import org.bukkit.Material;
import org.bukkit.command.Command;
import org.bukkit.command.CommandSender;
import org.bukkit.craftbukkit.v1_4_R1.inventory.CraftItemStack;
import org.bukkit.entity.Player;
import org.bukkit.plugin.java.JavaPlugin;

public class GlowWithEnchanting extends JavaPlugin {
    @Override
    public boolean onCommand(CommandSender sender, Command command, String label, String[] args) {
        if (sender instanceof Player) {
            Player player = (Player) sender;
            CraftItemStack test = CraftItemStack.asCraftCopy(new org.bukkit.inventory.ItemStack(Material.IRON_AXE, 1));
            
            addGlow(test);
            player.getInventory().addItem(test);
        }
        
        return true;
    }

    private void addGlow(org.bukkit.inventory.ItemStack stack) {
        ItemStack nmsStack = (ItemStack) getField(stack, "handle");
        NBTTagCompound compound = nmsStack.tag;
        
        // Initialize the compound if we need to
        if (compound == null) {
            compound = new NBTTagCompound();
            nmsStack.tag = compound;
        }
        
        // Empty enchanting compound
        compound.set("ench", new NBTTagList());
    }
    
    private Object getField(Object obj, String name) {
        try {
            Field field = obj.getClass().getDeclaredField(name);
            field.setAccessible(true);

            return field.get(obj);
        } catch (Exception e) {
            // We don't care
            throw new RuntimeException("Unable to retrieve field content.", e);
        }
    }
}

@nathanfranke I love your solution, thank you for posting it. Had no idea about item flags until now!