http://forums.bukkit.org/threads/ehm-allow-a-certain-player-to-use-a-command.302619/#post-2741029

Example.java

import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.bukkit.entity.Player;
import org.bukkit.event.EventHandler;
import org.bukkit.event.player.PlayerCommandPreprocessEvent;

/**
 *
 * @author Goblom
 */
public class Example {
    
    private static final Map<UUID, List<String>> allowedCommands = new HashMap();
    
    static {
        //lets pretend this is my uuid
        allowedCommands.put(UUID.randomUUID(), Arrays.asList("help", "msg", "tell", "pm", "tp"));
    }
    
    public boolean isAllowedToUse(Player player, String command) {
        List<String> commands = allowedCommands.get(player.getUniqueId());
        
        boolean canUse = false;
        for (String cmd : commands) {
            if (cmd.equalsIgnoreCase(command)) {
                canUse = true;
                break;
            }
        }
        
        return canUse;
    }
    
    @EventHandler
    public void onCommandPreprocess(PlayerCommandPreprocessEvent event) {
        //should return "help" instead of "/help"
        String command = event.getMessage().split(" ")[0].replace("/", "");
        
        if (!isAllowedToUse(event.getPlayer(), command)) {
            //This stoppes the command from being sent to the plugin that handles the command
            event.setCancelled(true);
        }
    }
}