For those that do not follow me on twitter (@pacifika), I've created a patched version of Textile, the html generator alternative to Markdown, to make it easier to use in CodeIgniter projects. I have provided the patch and patched Textile on support forums of both projects.
After patching, you can just use Textile like this:
$this->load->helper('textile'); $text = Textile("Dude this is *my* code!");
For more information read the post on the forums!