You can override basically all options directly in the theme by using http://www.zenphoto.org/documentation/functions/_functions-basic.php.html#functionsetOption and of course do that using if/else or switch depending on the current album.
Additionally you can use so called "album themes".
If you want options specific to a subalbum you would need to make use of the "custom data" field. If you wanted to do that via the themeoptions script you would probably want to create a custom handler. If you want to do it from the admin-edit pages then you might want to create a filter for the custom data.
Please see http://www.zenphoto.org/2008/04/zenphoto-plugin-architecture/ for further information on both these approaches. In addition, for the second approach you could review the plugin filter-customdata. This filter is new in the development stream, so if you intend to go this route, you will have to install the nightly build.