From Greebo.net there's a recent post that looks at converting the current database functionality in your application over to the MySQLi functionality and making use of prepared statements as a later of protection for your queries.

Okay, you've got like a zillion SQL queries in your PHP app, and probably 95% of them have a WHERE clause, and you need to make them safe so people will still download and use your app. Because if you don't fix your injection issues, I will rain fire on your ass. These are the steps you need to take to convert to prepared statements.

The guide is two steps you'll need to make the transition - "PHP 4 is dead. Upgrade to PHP 5" and "make sure your hoster has MySQLi". The major part of the update is under the first point where he gives code examples and suggestions to follow about how to "harden" your environment to prevent and issues that lax SQL methods might have caused and a simple example of a move from MySQL to MySQLi.