Waypoints or rather 5LNC (Five-letter-name Code) are issued by the ICAO ICARD (International Codes and Route Designators) System. States have a secure log in and when designing Instrument Flight Procedures and ATS Routes can request or select available 5LNC assigned for the purpose.
The first internet application of the ICAO International Codes and Routes Designators (ICARD) database was deployed in 1998. It was developed to support the allocation process of five-letter name-codes (5LNC) within the ICAO EUR/NAT region. The application was gradually extended to other ICAO Regions from 2005 onwards with ICARD becoming accessible to all ICAO Regions at the end of 2010.
Searching the ICAO site for ICARD gives some information and a description of how the 5LNCs can be selected is available on this link:
https://www.icao.int/NACC/Documents/...024Sep2014.pdf
The links to the public website for 5LNCs I believe have been disabled and you need a secure access now.