From the FAA Aeronautical Chart User's Guide

VFR Waypoint or a VFR Checkpoint?

VFR Waypoints and VFR Checkpoints are often confused, sometimes even in FAA documentation. Here's the difference.  VFR checkpoints have been around for decades and are always depicted on sectional charts with a small purple flag and a waypoint name.
VFR Waypoints are in the database of waypoints, VFR and IFR that GPS manufacturers program into their equipment.  But VFR waypoints don’t exist on IFR charts, so IFR pilots are unlikely to use them.  (But, they can if they want to).  Since VFR pilots can use any named coordinant they wish, the difference from waypoints and checkpoints tend to blur.
Pilots flying VFR would refer to a checkpoint by name when communicating with ATC, local airport base stations and even other VFR pilots.  It was a common identification that anyone listening would understand.  When a pilot qwould say that they are at 4,500 ft over Disney World, there was no question where the aircraft was located.  However, as more pilots were adding GPS equipment in their aircraft a new problem developed. 
VFR pilots were using the waypoints programmed into their GPS receivers, and they are all IFR waypoints.  As long as the aircraft were not in controlled airspace and they were at VFR altitudes, then this is perfectly legal.  However, consider the poor controller who had many aircraft converging on the same waypoint, many not "in the system", otherwise known as not participating in the available ATC services.  So the concept of VFR Waypoints came into the system.
So, here's a tip to remember the difference.  Waypoints are like breadcrumbs on a trail (without the birds).  You navigate from waypoint to waypoint, and those breadcrumbs are programmed into your GPS.  Checkpoints are where you "check in". 
VFR Waypoints are designed to help the VFR pilot avoid Class C, B and Special Use Airspace (SUA) incursions.  They are named using five characters, with the first two "VP".
The FAA has published a detailed explanation of the VFR Waypoint Chart Program.
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