IGN Cube is certantly hinting at just that. In there's most recent Mailbag update, somebody writes:
I saw my wishlist and I saw that the name for Metal Gear Solid for the GCN is MGS: Twin Snake. That means you know something, and I want to know what that is!!
-- Mike
Cory responds: Veeeerry interesting discovery. Yes, that could very well mean something. And it could be a very, very cool thing, indeed. Are we allowed to speak of it before E3? I'm afraid not. If we did, certain parties would have our tongues neatly removed and fingertips sanded clean off. In the case of my suction-cupped appendages, this would be very painful for yours truly.
He's Baaaaack
Those last 2 words were hidden in the bailbag(see for yourself
http://cube.ign.com/mail.html) Cleverly hidden indeed, but an obvious hint at MGS3.