In Free Battle or Mission mode hold L1 + R1 when you are choosing a character at the character selection screen.

Get the following rank to unlock the corresponding machines

Unlock Capsule Machine for Maniacs:
Achieve the rank of Anbu

Unlock Capsule Machine for Collectors:
Achieve the rank of Special Jonin

Get the following amount of Experience Points during the game to unlock the corresponding rank.

Unlock Genin Rank:
Get 50 Experience Points

Unlock Chunin Rank:
Get 500 Experience Points

Unlock Special Jonin Rank:
Get 1,150 Experience Points

Unlock Jonin Rank:
Get 1,750 Experience Points

Unlock Anbu Rank:
Get 2,170 Experience Points

Unlock Hokage Rank:
Get 2,490 Experience Points

Unlock Secret Characters
In Story mode using any default character complete his or her story to unlock a secret character and then complete the story with the character you have just unlocked to unlock another secret character.

Unlock Neji Hyuuga:
Complete Story mode with any default character.

Unlock Hinata Hyuuga:
Complete Story mode with Neji Hyuuga.

Unlock Haku:
Complete Story mode with Hinata Hyuuga.

Unlock Zabuza Momochi:
Complete Story mode with Haku.

Unlock Gaara:
Complete Story mode with Zabuza Momochi.

Unlock Orochimaru:
Complete Story mode with Garaa.

Unlock Alternate Costumes:
At the Selection screen when choosing a character hold L1 + R1.

Unlock Bonus 'S' Rank Missions:
Complete 'S' rank Mission 2, 'Icha Icha Paradise' to unlock Mission 11. To unlock Mission 12 complete ALL non-'S' rank missions (Hokage rank).