Change the "unknown command" message in 1.7.2 with ProtocolLib.

ChangingUnknownCommand.java

package com.comphenix.example;

import org.bukkit.ChatColor;

import org.bukkit.event.Listener;
import org.bukkit.plugin.java.JavaPlugin;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.JSONValue;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;

import com.comphenix.protocol.PacketType;
import com.comphenix.protocol.ProtocolLibrary;
import com.comphenix.protocol.events.PacketAdapter;
import com.comphenix.protocol.events.PacketContainer;
import com.comphenix.protocol.events.PacketEvent;
import com.comphenix.protocol.reflect.StructureModifier;
import com.comphenix.protocol.wrappers.WrappedChatComponent;

public class ChangingUnknownCommand extends JavaPlugin implements Listener {
    private interface Processor {
        public Object process(Object value, Object parent);
    }
    
    @Override
    public void onEnable() {
        ProtocolLibrary.getProtocolManager().addPacketListener(
            new PacketAdapter(this, PacketType.Play.Server.CHAT) {
                private JSONParser parser = new JSONParser();
                
                @Override
                public void onPacketSending(PacketEvent event) {
                    PacketContainer packet = event.getPacket();
                    StructureModifier<WrappedChatComponent> componets = packet.getChatComponents();
                    
                    try {
                        Object data = parser.parse(componets.read(0).getJson());
                        final boolean[] result = new boolean[1];
                        
                        transformPrimitives(data, null, new Processor() {
                            @SuppressWarnings("unchecked")
                            @Override
                            public Object process(Object value, Object parent) {
                                if (value instanceof String) {
                                    String stripped = ChatColor.stripColor((String) value);

                                    if ("Unknown command. Type \"/help\" for help.".equals(stripped)) {
                                        result[0] = true;
                                        
                                        // Add color to the parent object
                                        if (parent instanceof JSONObject) {
                                            ((JSONObject) parent).put("color", "red");
                                        }
                                        return "Wrong. Try again! Also note that we can apply a color to the " +
                                                "entire multi-lined messages, unlike ChatColor.RED.";
                                    }
                                }
                                return value;
                            }
                        });
                        
                        // Write back the changed string
                        if (result[0]) {
                            componets.write(0, WrappedChatComponent.fromJson(JSONValue.toJSONString(data)));
                        }
                    } catch (ParseException e) {
                        e.printStackTrace();
                    }
                }
            });
    }
    
    private Object transformPrimitives(Object value, Object parent, Processor processor) {
        // Check its type
        if (value instanceof JSONObject) {
            return transformPrimitives((JSONObject) value, processor);
        } else if (value instanceof JSONArray) {
            return transformPrimitives((JSONArray) value, processor);
        } else {
            return processor.process(value, parent);
        }
    }
    
    @SuppressWarnings("unchecked")
    private JSONObject transformPrimitives(JSONObject source, Processor processor) {
        for (Object key : source.keySet().toArray()) {
            Object value = source.get(key);
            source.put(key, transformPrimitives(value, source, processor));
        }
        return source;
    }
    
    @SuppressWarnings("unchecked")
    private JSONArray transformPrimitives(JSONArray source, Processor processor) {
        for (int i = 0; i < source.size(); i++) {
            Object value = source.get(i);
            source.set(i, transformPrimitives(value, source, processor));
        }
        return source;
    }
}

@DoctorDark: I believe I've fixed that error now. The trouble was that I assumed the root node of the JSON message would be a JSONObject, while in actuality it can be a simple string as well.

I've also addressed your chat color problem - if you add a "color" property to the parent JSONObject, the entire message will be colorized (see example).

@aadnk Why need transformPrimitives?