Remove equip limitations:
Pause the game at your school and press Right, Down, Left, Up, Left, Left, Left, Left, Y, Y, Y.

Extra Money:
Pause the game at your school and press Right, Down, Left, Up, Left, Left, Left, Left, Y, Left.

Extra Experience:
Pause the game at your school and press Right, Down, Left, Up, Left, Left, Left, Left, Y, Right.

Control camera view:
Pause the game during combat and press Up, Left, Down, Right, Left, Left, Left, Left, Up, Up, Up, Up.

Higher level enemies:
Pause the game at a League Office and press Right, Right, Right, Up, Up, Left, Left, Left, Left, Right, Up, Up, Up, Up, Down. Repeat to increase levels.

Lower level enemies:
Pause the game at a League Office and press Right, Right, Right, Up, Up, Left, Left, Left, Left, Right, Down, Down, Down, Down, Up. Repeat to decrease levels.

Increase HP:
Pause the game at a League Office and press Down, Right, Up, Left, Left, Left, Left, Left, Y, Up.

Increase defensive affinity:
Pause the game at a League Office and press Down, Right, Up, Left, Left, Left, Left, Left, Y, Left.

Increase offensive affinity:
Pause the game at a League Office and press Down, Right, Up, Left, Left, Left, Left, Left,Y, Right.

Normal timer speed in timed battles:
Pause the game at a League Office and press Right, Up, Left, Down, Left, Left, Left, Left, Up, Down.

Faster timer speed in timed battles:
Pause the game at a League Office and press Right, Up, Left, Down, Left, Left, Left, Left, Down, Up.

Berserk team:
Pause the game at a League Office and press Left, Down, Right, Up,Left, Left, Left, Left, Up, Right, Down, Left.

No random encounters:
Pause the game at the World Map and press Right, Left, Up, Down, Left, Left, Left, Left, Y, Y, Y.

Restore random encounters:
Pause the game at the World Map and press Right, Left, Up, Down, Left, Left, Left, Left, A, A, A.

Thanks to Revolution readers FloydFan and JuicyJuice!