Didn't know some of these myself...
Under the Weather -
If a crewman is standing watch on the weather side of the bow, he will be subject to the constant beating of the sea and the ocean spray. He will be
under the weather.
A Square Meal -
In good weather, crews' mess was a warm meal served on square wooden platters.
Let the Cat Out of the Bag -
In the Royal Navy the punishment prescribed for most serious crimes was flogging. This was administered by the Bosun's Mate using a whip called a cat o' nine tails. The "cat" was kept in a leather or baize bag. It was considered bad news indeed when the cat was let out of the bag. Other sources attribute the expression to the old english market scam of selling someone a pig in a poke(bag) when the pig turned out to be a cat instead.
No Room to Swing a Cat -
The entire ship's company was required to witness flogging at close hand. The crew might crowd around so that the Bosun's Mate might not have enough room to swing his cat o' nine tails.
At Loggerheads -
An iron ball attached to a long handle was a
loggerhead. When heated it was used to seal the pitch in deck seams. It was sometimes a handy weapon for quarrelling crewmen.
The Bitter End -
The end of an anchor cable is fastened to the
bitts at the ship's bow. If all of the anchor cable has been payed out you have come to the
bitter end.
Three Sheets to the Wind -
A sheet is a rope line which controls the tension on the downwind side of a square sail. If, on a three masted fully rigged ship, the sheets of the three lower course sails are loose, the sails will flap and flutter and are said to be "in the wind". A ship in this condition would stagger and wander aimlessly downwind.
Mind your P's and Q's -
In English pubs, ale is ordered by pints and quarts. So in old England, when customers got unruly, the bartender would yell at them to mind their own pints and quarts and settle down.
Bob's your Uncle -
A way of saying "you're all set" or "you've got it made." It's a catch phrase dating back to 1887, when British Prime Minister Robert Cecil (a.k.a. Lord Salisbury) decided to appoint a certain Arthur Balfour to the prestigious and sensitive post of Chief Secretary for Ireland.
Not lost on the British public was the fact that Lord Salisbury just happened to be better known to Arthur Balfour as "Uncle Bob." In the resulting furor over what was seen as an act of blatant nepotism, "Bob's your uncle" became a popular sarcastic comment applied to any situation where the outcome was preordained by favoritism. As the scandal faded in public memory, the phrase lost its edge and became just a synonym for "no problem."