Bingowings said:

2001 might not have them but the monolith builders become organic spacecraft on their way to becoming stitched from the fabric of the universe itself.

Alistair Reynolds, Iain M Banks, Anne McCaffrey, Peter F Hamilton.

Put on hold Babylon 5 for a minute and list almost any television Space Opera and it will have at least one.

Battlestar Galactica, Lexx, Doctor Who, Farscape, Blakes 7, Star Trek.

Then you have films like Alien, even the remake of Invaders Of Mars has a bioship for crying out loud.

It's a trope that's employed at least as much as hyperspace.

If you aren't aware of it you obviously don't read or watch enough science fiction.

Dude! - how could you leave out V-ger?

;-)