-Secret Message from Iwata.
When in Samus' ship, go to the radio And press the following symbols.
Going from left to right, press the second symbol, the seventh symbol, the fifth symbol and then the first symbol.
You'll be greeted by Iwata himself. Of course, this is in Japanese.

A brief translation...
Hello, this is Iwata from Nintendo.
A president has to take things really seriously, even if it doesn't seem like it. It's understandable if you lose weight from stress...but I get fatter instead. Nobody thinks I'm taking it seriously.
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-Secret Message from Miyamoto
When in Samus' ship, go to the radio and press the following symbols:
Going from left to right, press the eighth symbol, the third symbol, the fifth symbol and then the fourth symbol.
You will then hear a message from Mr. Miyamoto!

A rough translation:
Ah, can you hear me? This is Miyamoto.
All of you playing Metroid, can you hear me?
It’s fun, isn’t it?
I’ve also worked on many [Metroid] games, but this one is the best yet, don’t you think?
Definitely play it all the way to the end.
See you!
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-Bumper Stickers for your ship
Having these games on your Wii system memory will cause your ship to get decals when you enable the bumper sticker bonus:
Wii play
Wii sports
Zelda: Twilight Princess
Paper Mario
Metroid Prime 3