You can see a brief description of the differences here:
http://www.nessoft.com/multiping/beta.html.
The two products have relatively different uses:
Ping Plotter is a troubleshooting application, it looks for problems and lets you examine the route for the router causing the packet loss and latency.
MultiPing is a monitoring application, it lets you watch one or more destinations so you can decide which one is best to use, and also to monitor over time.
If you have more questions after reading the beta page above, please feel free to ask more questions.
- Pete