Mirage Island
Mirage Island is a secret island in the Sevii Islands. This island is a assigned an ID number once a day. If the ID number matches the ID number of one of your six main Pokemon, the island will reveal itself. To increase you chances of finding the island, switch all of your six main Pokemon out in-between searches for the island.
Free Premier Balls
For every 10 Pokeballs that you buy at a Pokemart, you will receive a free Premier Ball. These balls are much stronger than regular Pokeballs and are better at catching tough Pokemon.
Rayquaza
When you are in the Sky Pillar, if you have a Pokemon with the "Dig" command, you can use it at any point on the second floor to immediately find yourself at the top of the tower, face to face with the legendary Pokemon Rayquaza.
Corsola
In Pacificlog Town, there is a house with a girl standing beside it. In that house is a woman with a rare Pokemon called Corsola. If you have a Bellosom, you can give it to that woman for her Corsola.
Ralts
To capture a Ralts early in the game, find a small patch of grass on Route 102, outside of Petalburg City. Ralts will appear in this patch of grass.
Television
Watching any television can give you clues as to where you can go to find secrets or special deals on items. Commercials for the Mauville Game Corner, Lilycove Department Store or Slateport City Energy will indicate that you should go to that location to receive a special deal. You may also see reports of rare Pokemon in a certain area, at which point you should go to that area to catch the Pokemon.