I want Akismet to be activated by default on installation with my Akismet API key. I am making my own distribution that I will use on my own sites and I want the plugin and key to already be activated when installing a new wordpress site.
The link Bainternet provides looks quite promising. Now you only need to automatticaly add the API key. Akismet has a constant for this called *WPCOM_API_KEY* (source code).
So you could add something like this to your wp-config.php file and Akismet would use it as API key.