The Pokemon you place inside the Dream World have an effect on the place that you visit. For example, placing a Grass Pokemon in the Dream World will likely take you to the Pleasant Forest area, a Fighting type Pokemon will take you to the Rugged Mountain, a Water type will take you to the Sea etc etc.
Also, the number of badges you have in your game will also affect where you are sent.
If I understand correctly, after gaining at least 5 badges, all the areas become available, but I'm not 100% sure on that one.
But the program is great tool to have and use. I got my copy of Pokemon White 2 this morning, since it was released here today. I used the tool after gaining 1 Badge and it found 10 pages worth of Pokemon - granted that nearly all of them were the same ones on each page. Mostly all Druddigon, Aron, Goldeen, a Kabuto, 2 Basculin and some others. I chose a female Druddigon with Fire Fang. But already, I have 5 badges so I'll be testing it out tomorrow to see what I get then.