The funny thing with all this is whether or not Wii Sports or Wii Fit count, Nintendo is still the company with the best selling game. The right company gets the credit.
I say pack-ins don't count but only in the sense that the amount sold as a pack-in doesn't count. Some games are sold primarily as seperate titles and a limited-time bundle is also available. But the primary intention is for the game to be bought seperately so those count. I consider Wii Play to be an exception since it comes with a standard controller. Other bundles are always stuff where it comes with some special peripheral that that game is designed for. So it comes with a wheel or a lightgun or a guitar or a balance board. In that case the idea is more to buy the game and the accesssory required for that game. The idea isn't really to buy the accessory for a different purpose. The remote is a standard controller. Wii Play is not a special title that makes use of a special accessory.
My definition isn't a clear-cut rule. To me it's more case-by-case. It just seems obvious to me which titles hold a legitimate claim to their sales. Sadly, one of my favourite games of all time, Super Mario World, has tainted sales. Any of its GBA or VC sales though are legitimate.