In tikiwiki, a Plugin is generally an additional kind of page element to be used in the wiki mark up syntax.
They can most definately use PHP code, but are generally just snippets. For an example of that, have a look in the libs/wiki-plugins directory.
Stuff for tiki can also be packaged into "mods" which are installable by a tiki admin. The mods can then install files.
However, they cannot add new menu entries, so either the modules (units of displayed items to go in the side columns) or wiki plugins route is the way to get any of it actually linked in to the rest of a tiki site.