Try c3p0 or commons-dbcp. They both implement javax.sql.Datasource which is whitelisted by app-engine.
Example on commons-dbcp:
<bean id="dataSource" class="org.apache.commons.dbcp.BasicDataSource">
<property name="driverClassName" value="com.mysql.jdbc.GoogleDriver" />
<property name="url" value="jdbc:google:mysql://myappid:instanceId/mydb?user=myuser" />
<property name="username" value="myuser" />
<property name="password" value="mypassword" />
<property name="validationQuery" value="SELECT 1"/>
</bean>