I'm not sure I like the idea of a wrapper, because I like to be organized by directory and such, and I kind of like the users to see that reflected in the address, but I'll think about it.

That's where mod_rewrite comes in. You can make a URL of http://www.site.com/news/23/ map to http://www.site.com/index.php?f=news&id=23.

There's a tutorial here: http://www.alistapart.com/articles/succeed/