Extreme difficulty:
Beat the game on Normal.

Camera:
Beat the game once to unlock the camera. You can use the camera to snap shots during the game, some of which give you extra surprises.

Meryl demo mode:
Beat the game but do not submit to the torture.

Bandanna:
Beat the game but do not submit to the torture. At the end, Meryl will give you the bandanna, which gives you unlimited ammo.

Meryl outfit:
Beat the game twice and do not submit to the torture either time.

Otacon demo mode:
Beat the game but do submit to the torture.

Otacon outfit:
Beat the game twice and do submit to the torture both times.

Stealth and Tuxedo outfit:
Beat the game twice.

Different ending music:
Beat the game three times.

Thanks to Revolution readers Solidus and MGS Stud!