Spheal and Sealeo Bonus Stage
How to get:
Ruby: Get swallowed by the Wishcash that appears randomly (I think) in the pond
with the Chinchous and Lotads.
Sapphire: Press the P button some times and then throw the ball up the left
steel ramp to get carried by the Pelliper to this stage.
Time: 2'00"
Reward: Number of Spheals x 5,000,000 + Number of Pokeballs x 1,000,000

Duskull Bonus Game
How to get: It appears randomly after catching 3 Pokemon, in the hole in sapphire version only.
Time: 2'00"
Reward: 30,000,000

Kecleon Bonus Stage
How to get: It appears randomly after catching 3 Pokemon, in the hole in ruby version only.
Time: 2'00"
Reward: 30,000,000

Kyogre Bonus Stage
How to get: Getting HOLE after evolving, catching or hatching 3 pokemon. You can also get this on the HOLE slots. Sapphire only.
Time: 3'00"
Reward: 50,000,000 , Capture Kyogre (if beaten twice)

Groudon Bonus Stage
How to get: Getting HOLE after evolving, catching or hatching 3 pokemon. You can also get this on the HOLE slots. Ruby only.
Time: 3'00"
Reward: 50,000,000 , Capture Groudon (if beaten twice)

Rayquaza Bonus Stage
How to get: Getting HOLE after evolving, catching or hatching 3 pokemon.
Time: 3'00"
Reward: 99,999,999 , Capture Rayquaza (if beaten twice)