Although I don't own a copy myself, my favorite would be Paper Mario: The Thousand-Year Door. I played the game through when I visited my friend and even got on a higher level than he did :p After it went to random recipe fulfilling and badge seeking, I slowly stopped playing it when I went there.
I should have tried to complete the one hundred trials thingie (can't remember the actual name), though. I remember I tried it only once and lost very early.
After TTYD, I'll rank Mario Kart DS as the second best game :p It was the second DS game I bought (I have only WarioWare: Touched, Mario Kart DS and Pokémon Platinum as of now).