I've skimmed most of the posts in this thread, and I wanted to add this if it hasn't already been said:
There's only one N64 VC game out so far, but it's so generically mapped to the GC controller that I would anticipate all games will be mapped to the controller in the same way. (Yes, the D-Pad works in 2-D VC games, Super Star Soldier is confirmed by moi.)
HOWEVER - the Classic Controller is uniquely mapped in every game. That is to say that the A button on the controller could mean A in Mario but B in Zelda. You'll find this evidenced by hitting the Home button on the Wii Remote during a VC game and clicking the electronic manual. Here you will find a guide to how the controls are mapped on the Classic Controller and Wii Remote (if applicable) BUT NOT on the GC controller.
Edit: This means that you don't have to worry about all the C buttons in N64 games being automatically mapped to the second analog stick of the Classic Controller - expect Zelda to use the face buttons for items and not the control stick. However Turok could very easily have the C Buttons mapped to that second analog stick to give a simulation of dual analog FPS shooting, but who knows how they'll do that.
Nintendo obviously wants to sell Classic Controllers, and they want to emphasize that this is the controller that can do EVERYTHING on the VC (and hopefully elsewhere, considering that it has GameCube style analog L and R buttons that are useless for every VC game, indie stuff aside). So for those of you on the fence about the Classic Controller, know that it is fine tuned to every game. We MAY MAY MAY (probably won't) start doing some reviews of the VC games that come out so you can know if its unplayable with the Wii Remote or GC controller. Nintendo may start doing that soon.
FINALLY, did you guys know (you may) that you can suspend play on any VC game by hitting the Home button and returning to the Menu? Even if you turn the console off (and unplug it, I tried), the game will be right where you left it when you click it again. This is SUPER AWESOME.