the bilge is the part of a ship below the floor boards of the bottom level, just above the hull... ie the darkest and most grim part of the boat. a rat is, well, a small annoying (and to some people, scary) rodent. Therefore the term "bilge rat" is a pirate insult.

A Stoker or Spanner Wanker in the Royal Navy. Officially, they are Marine Engineering Mechanics or MEMs. Also, it's accurate since they usually spend a lot of time in the underbelly of a ship.