Which country's flag is the only one in the world that is flown in wartime, in a way that is different from how it is flown at other times?

The flag of the Philipines swaps the position of the red and the blue panels if the country is at war:

http://www.crwflags.com/fotw/flags/ph.html

You can only call the Union Flag the Union Jack if you have permission from the Queen! the flag can also be turned upside down so that you can tell others that you are in trouble without the enemy realising, this doesnt work anymore though.

Union Jack is a common name for the Union Flag. Union Flag is definitely correct terminology, whereas Union Jack is a little suspect. Although it is used even by UK Government publications to mean the Union Flag, that is, to the purists, a slang usage. Books will tell you that the original "Union Jack" was a Union Flag flown on a jackstaff (on a ship), though I'm not sure this is correct.

It is certainly true that flying your colours upside down is an internationally understood sign of distress (as distinct from flying someone else's flag upside down which is generally done to offend!) From a distance though it is difficult to see whether this is the case with the Union Flag. This is sometimes suggested as the reason that the versions of the flag commonly used at sea have the Union Flag design in the top left quarter, with the rest of the flag plain red, blue or white (depending on the type of vessel). Much easier to tell that has been reversed.

Did you know that you can only call it the Union JACK if it is on board a ship?