I think you are all forgetting an important element that makes goldeneye different from banjo, conker, and perfect dark... it is that goldeneye isnt an original IP created by rare, and as far as i know the only thing thats in the game that rare owns is the code, much like the donkey kong country series, sure rare made it, but because they dont own any property within the game itself, its up to the publisher to do what they see fit.
now im no law major but that seems to make sense to me. the fact is i believe this title has more to do with activision and the current movie studio holder (Metro Goldwyn Mayer?) in which case i dont think Microsoft/Rare has much of a say in this matter.
In addition to all of that, some of you may have remembered this January 11, 2006 IGN article:
http://wii.ign.com/articles/680/680846p1.html
where nintendo first revealed some in depth info regarding the VC service, anyway as you can see at the bottom that goldeneye is on the list of titles that are likely to be released.."early on". the fact that its on the list in the first place tells me that Nintendo knows goldeneye is very possible. and on top of that rare/microsoft hasnt said it wouldnt show up on VC and rare again did say some of those titles are possible.
so with all that evidence and what not i do believe there is a very good chance it will show up, though it may cost a bit more.