The Wii Remote fills this role naturally. A pointer swipe and button push gusts the wind into the world, lifting the small character to higher plateaus. Even ambient background objects like trees and grasses sway with the breeze. Later puzzles require you to guide the wind into other objects, not just the small fellow.
These techniques feel fresh and the visuals rival other Wii games. LostWinds was one of my favorite experiences from the Nintendo Media Summit.