Not complete answer but just a pointer...
QueryCounter
public class QueryCounter {
    private static long COUNTER = 0;
    private static long next() {
        return ++COUNTER;
    }
    private static String getHintValue() {
        return "/*Query No. " + next() + " */";
    }
    public static void setQueryCount(Query query) {
        /* EclipseLink */
        //query.setHint(QueryHints.HINT, getHintValue());
            query.setHint("eclipselink.sql.hint", getHintValue());
        /* OpenJPA + Oracle */
        //query.setHint("openjpa.hint.OracleSelectHint", getQueryHint());
        /* OpenJPA + MySQL */
        //query.setHint("openjpa.hint.MySQLSelectHin", getQueryHint());
    }
}
Usage
Organization sun = new Organization("Sun");
        em.persist(sun);
        tx.commit();
        Assert.assertNotNull(sun.getEntityId());
        Query query = em.createQuery("SELECT org.entityId FROM Organization org WHERE org.entityId = " + sun.getEntityId());
        QueryCounter.setQueryCount(query);
        query.getResultList();
        /*ServerSession does NOT log ReadObjectQuery??*/
        query = em.createQuery("SELECT org FROM Organization org WHERE org.entityId = " + sun.getEntityId());
        QueryCounter.setQueryCount(query);
        query.getResultList();
        query = em.createQuery("SELECT org.entityId FROM Organization org WHERE org.entityId = " + sun.getEntityId());
        QueryCounter.setQueryCount(query);
        query.getResultList();
Console
[EL Finest]: 2010-11-20 19:06:16.45--UnitOfWork(717879615)--Thread(Thread[main,5,main])--Execute query ReportQuery(referenceClass=Organization sql="SELECT entity_id FROM organization_tt WHERE (entity_id = ?)")
[EL Fine]: 2010-11-20 19:06:16.475--ServerSession(699542937)--Connection(1949550475)--Thread(Thread[main,5,main])--SELECT /*Query No. 1 */ entity_id FROM organization_tt WHERE (entity_id = ?)
    bind => [1]
[EL Finest]: 2010-11-20 19:06:23.372--UnitOfWork(717879615)--Thread(Thread[main,5,main])--Execute query ReadObjectQuery(referenceClass=Organization sql="SELECT entity_id, name FROM organization_tt WHERE (entity_id = ?)")
[EL Finest]: 2010-11-20 19:06:35.916--UnitOfWork(717879615)--Thread(Thread[main,5,main])--Execute query ReportQuery(referenceClass=Organization sql="SELECT entity_id FROM organization_tt WHERE (entity_id = ?)")
[EL Fine]: 2010-11-20 19:06:35.92--ServerSession(699542937)--Connection(1949550475)--Thread(Thread[main,5,main])--SELECT /*Query No. 3 */ entity_id FROM organization_tt WHERE (entity_id = ?)
    bind => [1]
OpenJPA has similar concept 1.8.7. Database-Specific Hints.
See if these specific hints can solve your purpose.
UPDATED ANSWER
@Eddie, see if this can help you...........
CustomLogFactory
    public class MyLogFactory extends org.apache.openjpa.lib.log.LogFactoryImpl {
    /* copied from LogFactoryImpl.NEWLINE */
    private static final String NEWLINE = J2DoPrivHelper.getLineSeparator();
    private boolean sqlLogger;
    @Override
    public Log getLog(String channel) {
        if("openjpa.jdbc.SQL".equals(channel)) { // OR equalsIgnoreCase(channel) ??? 
            sqlLogger = true;
        }
        return super.getLog(channel);
    }
    @Override
    protected LogImpl newLogImpl() {
        if(sqlLogger) {
            sqlLogger = false; /* once an SQL Logger is created, we dont't need any more instances */
            return new LogImpl() {
                private long sqlCounter = 0;
                @Override
                protected String formatMessage(short level, String message, Throwable t) {
                    if(isSQLString(message)) {
                        StringBuffer formattedMessage = new StringBuffer(super.formatMessage(level, message, t));
                        StringBuffer queryNo = new StringBuffer();
                        queryNo.append("  [Query # ").append(++sqlCounter).append("]").append(NEWLINE);
                        formattedMessage.delete(formattedMessage.length() - NEWLINE.length(), formattedMessage.length());
                        formattedMessage.append(queryNo);
                        return formattedMessage.toString();
                    }
                    return super.formatMessage(level, message, t);
                }
                /* just a sample implementation; checks whether message contains the word "executing"
                 * more concrete implementation should check the message for SELECT, UPDATE, INSERT INTO, ALTER.... clauses */
                private boolean isSQLString(String message) {
                    if(message.contains("executing")) {
                        return true;
                    }
                    return false;
                }
            };
        }
        return super.newLogImpl();
    }
}
peristence.xml
<property name="openjpa.Log" value="org.opensource.logger.MyLogFactory(DefaultLevel=WARN, Runtime=INFO, Tool=INFO, SQL=TRACE)"/>
Test
EntityManager em = Persistence.createEntityManagerFactory("default").createEntityManager();
EntityTransaction tx = em.getTransaction();
tx.begin();
Person person = new Person();
person.setName("Bond-OO7");
person.setAge(22);
em.persist(person);
tx.commit();
em.close();
Console
............
2084  default  TRACE  [main] openjpa.jdbc.SQL - <t 346613126, conn 1551158018> executing prepstmnt 556472773 SELECT SEQUENCE_OWNER AS SEQUENCE_SCHEMA, SEQUENCE_NAME FROM ALL_SEQUENCES  [Query # 1]
2136  default  TRACE  [main] openjpa.jdbc.SQL - <t 346613126, conn 1551158018> [52 ms] spent
2305  default  TRACE  [main] openjpa.jdbc.SQL - <t 346613126, conn 2026561073> executing prepstmnt 6637010 INSERT INTO Person (id, age, name) VALUES (?, ?, ?) [params=?, ?, ?]  [Query # 2]
2306  default  TRACE  [main] openjpa.jdbc.SQL - <t 346613126, conn 2026561073> [1 ms] spent
............