Plug-In Installation Locations
There are three ways that you can install FileMaker plugins, depending on where you need them to run.
FileMaker Pro (Windows or Mac)
This is the standard place that you're used to putting plugins. These plugins will run in the FileMaker Pro client software.
FileMaker Pro/Extensions
FileMaker Web Publishing Engine (Windows or Mac)
You would install plugins on the Web Publishing Engine in order to invoke them from Instant Web Publishing or Custom Web Publishing. On FileMaker Server 9, the Plugins folder may not exist - just create it and put the plugin there. All 360Works plugins will run in the Web Publishing Engine.
FileMaker Server/Web Publishing/publishing-engine/wpc/Plugins
FileMaker Server (Windows or Mac)
For most plugins, the primary reason to install them on FileMaker Server (this is NOT the same thing as the Web Publishing Engine) is to use them with scheduled scripts in FileMaker Server 9 (this feature is not available in earlier versions of FileMaker Server). There are a few plugins, such as AdminAnywhere, which perform other functions on the server. All 360Works plugins can be used with scheduled scripts in FileMaker Server.
FileMaker Server/Database Server/Extensions directory