This is a good question because I hear this pretty frequently; only black and blue pens can be used. Here's what the SQF Code Says:
"220.127.116.11 All records shall be legible and suitably authorized by those undertaking monitoring activities that demonstrate inspections, analyses and other essential activities have been completed.
18.104.22.168 Records shall be readily accessible, retrievable, securely stored to prevent damage and deterioration and shall be retained in accordance with periods specified by a customer or regulations."
By that code, you can use any color you want. This is what I've always done - I've not found the need to over-complicate things. That being said, however, the code doesn't state that you need to use a pen at all. Does that mean someone can sign in pencil? I know of no auditor that will be very understanding to using pencil (or anything that can be erased).
That being said, I've had no complaints ever about pen color, even without having a defined pen color program. I think if you have an SOP that uses color coding on pen color to convey information, you will not be questioned about it.