There are a wide range of plugins available in Geneious. These plugins offer additional functionality and can be installed through the Plugins menu (Tools→Plugins).
The location of a plugin in Geneious once it is installed will depend upon the function of the plugin. For example, the plugins for tree builders (eg. Phyml, Paup* and MrBayes) will appear as options in the "Tree" menu, whilst the GenBank submission plugin is available through the Tools menu (Tools→Submit to GenBank). Other plugins are tied to a particular document type and the functions will appear when you open a file of that type. For example, the microsatellite functions will appear when you open a microsatellite document in Geneious.