So I've gotten the 3ds for christmas, and I've had no problems registering it on club nintendo, nor any problems registering the zelda game it came with. ( Bundle) , but when I try to register anything else I get the invalid message. Now I've been trying to register some wii games that I know are eligible as I've looked on the list they have up there, and nothing seems to work. It's become quiet frustrating and I'm not sure if maybe I'm putting the PIN code in wrong or what. If any one could possibly help, I'd greatly appreciate it. Thanks.

Couple of ideas off the top of my head:

Codes have expired;
Codes aren't being entered correctly, O as 0 etc.

OK, that's all I've got.

There shouldn't be anything wrong with your new 3DS, perhaps the code you entered initially was just wrong.

Your other games, such as the Wii games you mentioned could have expired.
For example I mistakenly waited to register one of my Wii games published by Nintendo and it turns out there was an expiration date for doing the survey.
If I remember correctly you can still do the survey, you just won't be able to get any coins.

I am not sure but if games have already been registered can they be registered again at Club Nintendo. Like if I buy a used copy of Skyward Sword for example.

Nope. Codes can only be used once.

If the game is used then its a good chance that the code it already used too
Thats Club Nintendo for you but...

At Club Sony you will never have that problem and they even mail you free bacon every moring!

Its possible that you got a hacked code this happened to me too (this happens when somebody got the code by trying) in this case youll have to send the sheet of paper with the code and a copy of your receipt you got while buying in the store or online shop and send them by mail to your Nintendo consumer service team