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 apples and 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 however cocoa beans can be spawned in MineCraft Edit if you set ID to 351 and Damage to 3. The other two non-spawnable items are the two other kinds of saplings, and brown wool.