On the cruise track there is one in the hole underneath the upper deck
That one isn't a short cut, IIRC, it's an alternate route - that from my memory was slightly slower than the normal way.
Umm. There's an obvious shortcut in the Waluigi(or Wario) Stadium. Whichever one was really long and had two laps. You go over the huge hole near the end with the rainbow-booster, rather than going around either way.
On the desert level there is a shortcut that requires two mushroom boosts. At the start of the level turn right a little in and use your boosts to cut across the section. Don't go too far into the darker dirt, because that's an out-of-bounds.
on the DK level, go to the right of the track when it gets bumpy when you reach the mountain. It should be smooth. You go faster on smooth ground rather than bumpy ground.
On the final pass on the city-ish level, if you have a boost, the veryyyy right of the hole- there is enough to drive on. You go too slow without a boost.
On the yoshi level you can jump the first pit with a boost. (Also works in MKDS with snaking)
uhh. There's probably a lot more I'm forgetting. A stop by gamefaqs.com will probably tell you them all.