My answer is obvious of course. Galaxy is by far the best to me. I was never into the freeform exploration of 64 and Sunshine, it didn't feel like Mario to me. Galaxy feels like a 3D Mario should, the true evolution of the 2D games.
If I had to give them number scores, I'd give Galaxy a 10, 64 a 8.3 and Sunshine a 7.4.
What do you think? Who is your favorite?
Top 3 favorite games: Super Mario Galaxy, The Sims 2 (PC), The Legend of Zelda: The Wind Waker