Here is my hibernate.cfg.xml:

<?xml version='1.0' encoding='utf-8'?>
<!DOCTYPE hibernate-configuration PUBLIC
"-//Hibernate/Hibernate Configuration DTD 3.0//EN"
"http://hibernate.sourceforge.net/hibernate-configuration-3.0.dtd">

<hibernate-configuration>

<session-factory>

<!-- Database connection settings -->
<property name="connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="connection.url">jdbc:mysql://localhost/golf</property>
<property name="connection.username">XXXX</property>
<property name="connection.password">XXXX</property>

<!-- JDBC connection pool (use the built-in) -->
<property name="connection.pool_size">1</property>

<!-- SQL dialect -->
<property name="dialect">org.hibernate.dialect.MySQLInnoDBDialect</property>

<!-- Enable Hibernate's automatic session context management -->
<property name="current_session_context_class">thread</property>

<!-- Disable the second-level cache -->
<property name="cache.provider_class">org.hibernate.cache.NoCacheProvider</property>

<!-- Echo all executed SQL to stdout -->
<property name="show_sql">true</property>

<!-- Mappings of hibernate persistent classes -->
<mapping resource="golfbase/Holes.hbm.xml"/>
<mapping resource="golfbase/Courses.hbm.xml"/>

</session-factory>

</hibernate-configuration>

It doesn't seem to be loading the Holes.hbm.xml, since I keep getting:

0 [main] ERROR golfbase.golfBase - org.hibernate.MappingException: Association references unmapped class: Holes

when I attempt to run my app. If I delete the courses mapping, then holes attempts to load and complains that courses is missing. Is there something I need to do to load more than one mapping?

I am not sure but the order of the mapping files in your hibernate configuration might make a difference did you try yo change te order ????
are all the maping files in the maps?

What do you see in the output/log from hibernate????
If ou don´t have logging try to include it and maybe change to
debug level.

Good luck!