Johannes Schluter's Blog: Changes in PHP trunk: No more extension for sqlite version 2
Johannes Schluter has a quick new post to his blog today talking about parts of the sqllite extension that will be dropped from the core - the current sqlite_* methods and the pdo_sqlite driver.
The issue there is that this depends on the SQLite 2 library which isn't supported by upstream anymore for a few years. It was a logical step therefore to remove this extension from PHP trunk. The support for the sqlite3 extension and the PDO_sqlite driver (same link as above, read it carefully), which use version 3 of the library, are continued.
The change probably won't be happening in any of the PHP 5.3.x releases but should becoming in PHP 5.4 so, as he advises, you might need to rebuild your database file and change your application to correct things for the changes.