This version wraps the Community version with a focus on the underlying data model, as well as several useful UI features such as layouts, and a widget that offers pan/zoom functionality. It provides a fast way of building an application with visual connectivity at its core.
The Toolkit version has a commercial, per-developer, license with optional access to the source code and to email support (plus updates to new released versions for a year). License terms are available here.
This is the open source jsPlumb project hosted on GitHub that was first created in early 2010. It is a view technology only, providing an API for configuring connectivity between elements of your UI. The Toolkit edition uses this as the view layer for connectivity, so this documentation will be of use to you when using either edition.
This version of jsPlumb is where all current future functionality relating specifically to connecting DOM element does and will reside. Development of this version will continue concurrently with the Toolkit version.
The Community Edition is licensed with the MIT or GPL2 license; you choose whichever suits your needs.