Unlock Characters
The following characters can be unlocked by completing the said number of missions:

Akamaru - Complete 25 Missions
Anko - Complete 50 Missions
Awakened Hinata - Complete 100 Missions
Haku - Complete 40 Missions
Iruka - Complete 15 Missions
Itachi - Complete 55 Missions
Karasu - Complete 35 Missions
Kimimaro - Complete 30 Missions
Mizuki - Complete 20 Missions
Orochimaru - Complete 65 Missions
Sarutobi - Complete 85 Missions
Sasuke: Cursed Seal 2 - Complete 120 Missions
Tayuya - Complete 10 Missions
Tsunade - Complete 75 Missions
Ukon - Complete 5 Missions
Zabuza - Complete 45 Missions

Starting bonus
Have a saved game file from Naruto: Gekitou Ninja Taisen! 3 on your memory card to begin the game with the Omake option and all versus handicaps unlocked.

Difficulty 4
Unlock Shadow mode then complete the "B" rank mission "Beat 50 Shadow", the "A" rank mission "Beat 100 Shadow", and the "S" rank mission "Beat 200 Shadow.

Mission mode
Successfully complete Story mode part 1.

Shadow mode
Play Survival mode twenty times.

Gallery in Omake mode
Successfully complete Story mode parts 1, 2, 3 and 4. Note: You wil see Kakashi putting up posters.

Cancel combo to do other combos
Press [Y] at a certain time during a combo to cancel it.

Glitch: Fireball
First, unlock Unsealed 2 Sasuke. Then, start a versus match where both players chose him. Have both people fill their Chakra meter. Once both meters are full, have both players simultaneously press [Down] + [X] to trigger his secondary special, the Katon. If they are far enough apart (medium distance), the two fireballs should collide and become suspended in mid-air. The fight will continue as normal, only darker and extremely lagged. Also, sometimes by running into your opponent's fireball, you can take the damage with the fireball still there (although this might only work the first time).