The real answer is........ Whoever is constructing the particular piece of airspace.
For example, in the UK, the waypoints are usually associated with an actual location underneath or nearby, i.e Wellin - Wellyn Garden City, Upton - the village of Upton, etc.
However, there are also ones which are invented on a whim:
The helicopter routes out of Humberside have Milde, Lager and Bitta - also used to have Beere as well.
Off the subject slightly, but there also a number of North Sea oil and gas rigs which are named after the Thomas the Tank engine characters, (Gordon, Edward, Thomas etc).
