I created a Markdown plugin for Serendipity. Markdown is a simple, yet powerful plaintext to (X)HTML converter, originally written in Perl; but there is a PHP port. Basically, I copied the BBCode plugin, ripped out some unneeded lines of code, changed some strings and integrated the library file.
The installation is pretty straightforward. Get the latest PHP-Markdown, put the markdown.php file into your $serendipitypath/bundled-libs/Markdown/ directory. Now get my plugin and extract it into your $serendipitypath/plugins/ directory.
Now choose the Markdown plugin from your plugin list in the S9Y admin interface. You might want to disable other text formatting plugins, if you encounter any problems applying the markdown syntax.
I don’t know yet, if that is the correct and preferred way to go in S9Y, but it works for me[tm]. And I hope the S9Y folks can tell me, what to improve.
It appears that it works for others too ;-)
The plugin is available for all S9Y users through SPARTACUS, the secondary extension installer for Serendipity. No need to download and configure it yourself, just do the two clicks in the plugin administration (You might want to install SPARTACUS first, though).
 Version 0.8 or higher.