Good ideas
Personally, I'd enjoy a "developers' commentary" sort of like Monolith did for the special edition of F.E.A.R. It'd be pretty neat to play the game, and then watch the 3DR guys play through select parts and discuss them. We'd probably get to hear a lot about the original 2001 version of the game, too, which would be cool.
As for toys and the like, well, a Duke figure would rock. Like, a pewter figurine (I believe they did something similar to that for Doom3's release). A mousepad is a good idea, too, but I probably wouldn't use it for fear of spilling soda on it or something. A mini-comic, mini-soundtrack, or even a mini-artbook would also be pretty neat; something filled with conceptual sketches from 2001 to the current iteration would be quite the bonus.
Well, those are some ideas. I hope 3DR picks a few of them