See here for explanation of what they are: http://pokemondb.net/pokebase/22152/what-is-an-shaking-bubbling-spot
Either the grass will be shaking, water will be bubbling, or sand will be thrown up (in caves).
All you need to do is walk onto the spot and you encounter a rare pokemon. On the water you can also go next to the spot and fish on it.
However, be careful because you can often run into another pokemon on your way there, then the shaking spot will be gone!