G'day Badmachine,
Waypoints are waypoints, and can be used by any nav computer. A GPS is not a nav computer as such, it is a sophisticated radio receiver with a built in nav computer. Any waypoint can be used by any nav computer as long it is stored in the database. There are really no GPS specific waypoints.
Some of the B767s I fly have a GPS position update capability which is used by the FMC to refine the accuracy of the raw IRS position, some don't and rely on radio navaid position, RNAV, updates.
Waypoint information come from a database, or be transmitted to an aircraft by ACARS or be manually inserted by using Lat/Longs.
WAAS is a ground based GPS supplemental system to give better coverage and further refine the satellite GPS data for use in particular terminal areas.
Regards,
BH.