I like Wuhu Loop. The scenery is excellent, and the whole island is one of my favorite locales in a Nintendo game. Maka Wuhu is fun, too, but the glitch shortcut kind of ruins it for everybody.
I like Wuhu Loop and Rainbow Road the best because I love the new loop race style instead of just laps. I also like going on that bridge that reminds me of the Golden Gate Bridge.
I would say Rainbow Road followed by Bowser's Castle. Both are amazing courses. Also, the Star Cup is something to die for and the first three tracks from the cup all rank extremely high on my list. And let's give the Retro Tracks some love and throw in Rainbow Road (SNES) and Airship Fortress (DS).