Get the following achievements on missions to unlock the corresponding effect

Unlock Super Shuriken:
Get a Grand Master rating on Mission 1

Unlock Exploding Arrows:
Get a Grand Master rating on Mission 2

Unlock Chameleon Spell:
Get a Grand Master rating on Mission 3

Unlock Flash Bomb:
Get a Grand Master rating on Mission 4

Unlock Dog Bone:
Get a Grand Master rating on Mission 5

Unlock Invisibility Spell:
Get a Grand Master rating on Mission 6

Unlock Fire Spell:
Get a Grand Master rating on Mission 7

Unlock Viper Potion:
Get a Grand Master rating on Mission 8

Unlock Ninja Armor:
Get a Grand Master rating on Mission 9

Unlock Fireworks:
Get a Grand Master rating on Mission 10

Unlock Decoy Whistle:
Get a Grand Master rating on Mission 11

Unlock Binding Spell:
Get a Grand Master rating on Mission 12

Unlock Semimaru:
Get a Expert Ninja ranking on ALL of Rikimaru's levels

At the Title screen enter the following cheats.

Unlock All Characters
Hold White + Black and enter:
Up, Right, Left, Down, release White + Black and enter L, R

Unlock B-Side Audio
Hold L + R and enter:
Down, X, X, Up, X, X, Left, X, X, Right, X, X

Unlock 'Through the Portal' Bonus Rikimaru Mission:
White, Up, Black, Down, L, R, Left


During Gameplay Cheats
Enter the following cheats after pausing gameplay.

Boost Score:
Hold White + Black and enter Right, Right, Right, Left

Boost Offense:
Hold R + White and enter Up, Down, Up, Down

Display Score:
Right, Right, Right, Left

Full Kuji meter
Hold R + L and enter:
Left, Left, Left, Right, X

Get one Kanji:
Left, Left, Left, Right, X

Restore Health:
Up, Down, Up, Down, X, X, X

New Special Ability
Hold R + Black and enter:
Up, Up, Down, Down, release R + B and enter X, X, L

Item Cheats
At the Ninja Item select screen enter the following cheats.

All Ninja Items:
Hold R + L and enter:
Up, Down, Up, Down, X, X, X, Left, Right, Left, Right, X, X, X

Infinite Capacity:
Hold R + L + White and enter:
Up, Up, Down, Down, Left, Right, Left, Right, release White and enter X, X, X

More Ninja Items
Hold R + L and enter:
Up, Left, Down, Right, X, X, X

Mission Cheats
Enter the following cheats at the Mission Select screen.

Open all Layouts
Click Right Analog, Click Left Analog, L, R, White, Black

Unlock all Missions:
White, White, L, R, Right, X, Click Left Analog, Click Right Analog