System Message Control Tool 

This add-on breaks up a lot of the system messages (the yellow ones) into groups, which you can then decide to send to different chat windows, change the color of them or simply mute them.
It also breaks up various other messages, like the guild messages (normal, officer and MotD), into their own groups, so you can set which chat windows they should show in and in what colors.
Note that regarding the guild messages those are being set through the default chat system (right clicking the chat tab), where all others are controlled from the SMCT option window.

No message will ever be "lost" if you, for instance, delete a chat window and forget to change the setting for some message group. In that case the message will just be sent back to the original chat system to do its default behaviour.

If you want to just change the color of a message, you will have to still set which chat window it should go to. If you just leave it at "Pass-through" the system will ignore the group to speed up processing of messages.

The "Pass-through" option will just send the message back into the original chat system for it to do whatever it's setup to do, so this setting is used for all the messages you just want to act as they do now.

To access the options just type "/smct".

Note:
This has not been fully tested on non-english clients, but it should however work since everything is parsed from the pre-defined variables within WoW.

If you find any messages missing, please give me the exact message and what you did when you got it so I can add it to the system.

The amount of message groups in the system now is rather substantial. I will reorganize them and improve the overall GUI to handle them better, providing a better overview.
Improvements to the profile copy system is coming too.