Monkey mask and Banana camouflage:
Beat all Snake vs Monkey record times.

Snake's nightmare:
When Snake is caught in Groznyj Grad save the game, then load the save file.

Skip The End's boss fight:
There's an area where you must swim across some open water to some guarded docks, and you can kill The End here if you use the Dragonov to shoot him and his guard immediately after the cut-scene in which he is wheeled out to the docks.

Another way to skip The End:
When your battle against The End begins, save the game. Then, restart your PS2 and set the system clock ahead one week. When you resume the battle, you'll get a calling informing you The End has passed away.

Fun with the X-Ray:
Go to the cure screen and tap R1 twice.

Bonus Snake vs. Monkey levels:
Beat the game.

Snake barf:
Go to the character viewer, spin Snake around for awhile, then press Start.

R1 during the ending:
There are unmarked portions of the ending sequence where you can use the R1 button.

Time paradox:
After the cut-scene where you first encounter Ocelot, cut him up and the game will end due to a Time Paradox.

Killer bees:
Beat the pain by draining his stamina to get the hornet uniform. Then, with the hornet camo equipped, stand under a bee hive and shoot it down. As the bees are swarming around you walk over near an enemy.

Alert frequencies:
If you grab a guard and interrogate him during an alert he'll give you a frequency to call that will cancel the alert.

EZ gun:
Collect every type of plant and animal in the game.