Taken from an online sea faring man's website:

"Let me explain the reason and the meaning behind Poop Deck. The term "Poop Deck" refers to the partial deck above the ship's main afterdeck at the stern of the ship. In the days before indoor plumbing, a structure was rigged aft of this deck over the sea for the purpose of relieving oneself. When a ship takes a wave over the stern of a ship it is said to be "pooped." For the purpose of these pages, "Poop" means having the inside information. I'm not sure where that particular term originated, possibly the Poop Deck was also a place to exchange information. If anyone has the straight "poop" on the origin of that last definition, please let me know."

ED NOT: I know from personal experiences from my younger days as a pirate that there (used to be) a drinking establishment called "The Poop Deck" in Galveston, Texas, and can vouch for the authenticity of villians and rucous behavior in such a place. RRRRRRRRRRRRRR! Yes, many things happened at the Poop Deck. Many many things indeed.