jedi have the ability to sense "vergences" in the force. in TPM, when Qui-gon tells Mace he has found a vergence in the force, Mace asks, "centered around a person?" This implies vergences in the force can be centered around places as well. Yoda found a place where there was a dark side vergence and set up camp there to avoid detection. Its somewhat unlikely that the EU explaination of the dark presense there will be the one GL uses in EPIII.
The cave thing is completely EU. During the Old Republic times (before and during the Prequels), many Jedi on B'phashi went bad and became Dark Jedi. One of the Dark Jedi went to Dagobah and Yoda killed him. The Dark Side powers of the Dark Jedi took over the cave and tree there. This masked Yoda's existance.
How Yoda ended up on Dagobah is a mystery to us. It will most likely be told through the events of Episode III and maybe EU connecting Ep. III with Ep. IV, A New Hope.