I prefer just allowing HTML (though securing it using HTML Purifier, an excellent yet underused tool) and perhaps add WYMeditor for easy markup. However, Wikipedia knows quite a few and I suppose most of them also have PHP ports or are PHP native, such as TextilePHP.
Thanks both for your answers. I was considering using Textile, but it’s too bloated for what I need it for really (although very good), and lefteh’s suggestion is the road I was going down if I didn’t find anything. I guess I’ll be writing my own then.