Actually with the release of Geeklog 2.1.1 plugins can support multiple themes and a set of plugin templates can be based on other templates. The core plugins and the forum support this. The forum is the only plugin at the moment that actively uses this. We added this so plugins can be upgraded with out wiping out any custom template and css changes.
The plugin template theme directory can also have a functions.php file now. Take a look at:
for an example.
If you are developing a Geeklog theme if you want you could also include the template files for the plugin right in the root of the theme directory under a directory named after the plugin (like forum). You can only include the template files you want changed as if any are missing it will fall back to the default template files for the plugin.
More information can be found on the wiki http://wiki.geeklog.net/index.php/Theme_Developers_Guide#Theme_Specific_Plugin_Templates
One of the Geeklog Core Developers.