If you want to use SQlite3 databases with PHP you should probably use PDO.
Install it like this:
su apt-get install php5 php5-sqlite echo -e "\nextension=pdo.so\n" >> ../conf/php.ini
Note: You don't need any command like
pecl install pdo_sqlite or
pecl install pdo as PDO is now included in the package
php5-mysql). In my case this broke my PHP installation and I had to run the following to get it back working:
su pecl uninstall pdo pdo_mysql pdo_sqlite apt-get reinstall php5-common php5-sqlite
For examples see the invoices project.