For pure motion Skyward Sword. The breath and accuracy of its use of motion remains astounding. The best swordplay in any game, pointer controls for the slingshot combined with true motion for the bow a la Wii Sports Resort, the beetle, ect. Enemies that would always blocked you if you just waggled and didn't put real thought and effort into it. And it managed to make cleaning with the gust-blower fun.
For pure IR Resident Evil 4 and Metroid Prime 3. Both were just so much better and more responsive than their Gamecube versions it is impossible to go back. Prime 3 in particular has the best controls I've ever seen in an FPS game, including on PC. It may not be as customizable as other games, but it feels fantastic, the 60 FPS helps, it's use of the Prime lock-on system compliments the motion controls while still requiring the player to aim, and the addition of the grapple beam into combat really ups the immersion.
Wii Sports Resort nailed most of its games so well. Even canoing was fun. The only real stinker was cycling.
The Exite games Truck and Bots had better motion steering than Mario Kart.
The first 3 Madden games and the last few Tiger Woods games had amazing controls for sports games, I'd say Tiger Woods 10 and 11 for the Wii are the best Golf video games ever made.
Red Steel 2 doesn't have the best gunplay on the Wii, and Skyward Sword arguably did swordplay better, but both were still done well enough that the way you could switch between them was awesome.