A pen is a writing instrument which applies ink to some surface. There are two ideas about where the word pen came from.

Originally the word meant quill, and is derived from pinna (Latin for feather. Pens were made from goose feathers by carving the fearther with a penknife
The inventor of the first pen (which was a mechanical graphite pencil) was Slavoljub Penkala and the device was named that way. It's abbreviated form is 'Pen', the first three letters of the inventor's surname.

Penkala later invented and perfected the fountain pen. Both devices are patented:

The patent for the mechanical pencil was obtained in 1906. from the Royal Patent Office in Budapest, patents No. 36946 and 38353. The patent was registered in England as No. 3690/1906 and 183242.
The fountain pen goes under patent no. 193717 DRP.

Types of pens currently in use include the ballpoint pen, the fine-line marker pen, the artist's pen, and the fountain pen. Pens are also known, although not very commonly,as frindle.

Things that could be mentioned here

invention of the cartridge pen
invention of the biro
the space pen
the (possibly urban-mythical) tale of the Russians using a pencil in space instead
contrast with brush

A pen is also the term used for the much-reduced and entirely internal shell of some cephalopod mollusks, especially squid.

Pen is also used as a verbal expression of "to create" or "to write".

For example: "Today, I think I'll pen the Great Canadian Novel."

Pen is also used to describe an enclosed location.

For example: Pigpen

Short for penitentiary.