On startup VE3D looks in the Plugins folder of the install directory (ProgramFiles\Virtual Earth 3D) and iterates through the assemblies in each subfolder of Plugins. A plugin named Sample would install itself as C:\Program Files\Virtual Earth 3D\Plugins\Sample\Sample.dll. Note that this folder doesn't exist by default so your plugin installer will need to create it.
Next each assembly is probed for classes that descend from Microsoft.MapPoint.PlugIns.PlugIn. For security reasons only assemblies that are in the GAC are allowed to run. The good news is that we are investigating allowing partially trusted plugins for our next release. This means you will be able to visit a website and have it load its own plugins to add new functionality to VE3D without forcing you to go through an install process. Since we're still in the early parts of our next release I don't know for sure if this will make the cut but it is something we would like to add.