Well, first and foremost, the standalone version is free! It doesn’t allow direct integration with hosts or clips but both versions use the same interface and allow you to render video files of your particle projects. Projects can also be shared between standalone and plugin versions.
Another main difference is the plugin version allows you to directly composite particles over source footage in a supported host application. It also gives you access to the integrated Mocha motion tracking and masking, Beat Reactor, Glow and more.
Both plugin and standalone versions share the exact same emitter (presets) library,
This video covers more of the differences between the two versions.