All bonuses:
Quickly press R3, L3, R2, L2, R1, L1, Square, Triangle, Circle, X, R3, L3, R2, L2, R1, L1, Square, Triangle, Circle, X at the title screen.

Alternate costumes:
Have a saved game file from The Oanechan Bara to start with Saki's, and all of Aya's original five costumes unlocked.

Aya original costume 1:
Complete five quest mode quests in story mode.

Aya original costume 2:
Complete six quest mode quests in story mode.

Aya original costume 3:
Complete seven quest mode quests in story mode.

Aya original costume 4:
Complete eight quest mode quests in story mode.

Aya original costume 5:
Complete nine quest mode quests in story mode.

Aya 2:
Complete two quest mode quests in story mode.

Hard mode:
Complete level 6 in story mode under the normal difficulty setting.

Violent mode:
Complete level 6 in story mode under the hard difficulty setting.

Makoto:
Complete level 6 in story mode as Riho.

Makoto 2:
Completely fill the ???? gauge.

Riho (17):
Complete ten quest mode quests in story mode.

Saki:
Complete level 6 in story mode as Aya.

Saki original costume:
Complete four quest mode quests in story mode.

Saki 2:
Complete three quest mode quests in story mode.

Wallpaper 1:
Complete one quest mode quest in story mode. Then, press L1, L2, R1, or R2 at the mode selection screen to switch to the new wallpaper.

Wallpaper 2:
Complete level 6 in story mode under the hard difficulty setting. Then, press L1, L2, R1, or R2 at the mode selection screen to switch to the new wallpaper.

Wallpaper 3:
Complete level 6 in story mode under the violent difficulty setting. Then, press L1, L2, R1, or R2 at the mode selection screen to switch to the new wallpaper.