Cocoa Beans

Cocoa Beans (also known as the Brown Dye) are a material used for making Cookies and brown wool. Cocoa Beans were initially introduced in the Beta 1.2 update, but were not able to be obtained without an Inventory Editor.

As of Beta 1.4, Cocoa Beans were formally brought into the game as a reward found in dungeon chests. (80% Chance) Also as of Beta 1.4, brown sheep naturally spawn which made obtaining brown wool easier.

Jeb Said during his Dreamhack presentation that cocoa trees are pending. Cocoa Beans are among the rarest obtainable items on old maps (after cookies) as they can only be found in dungeons generated after the 1.4 patch. The use of cookies as a 'trophy item' gives cocoa considerable value on unmodified servers, even more so than diamonds.

Cocoa beans are one of the four items that can only be obtained by legitimate means on SMP, because they have the same data value as ink sacs, but there is no way to craft them, unlike the other dyes. In other words, you cannot simply spawn them with server commands as this would result in getting ink sacs instead, due to sharing a data value. This can be avoided by using a mod to enable defining of the damage value of an item given with the /give command. (Before 1.0)

Trivia

 * In snapshot 12w03a Cocoa Bean Pods can be seen on jungle leaves, Jeb has stated he might be adding them as a drop from leaves much like Apples if he can find a way for players to farm them.