Look at the various "JNDI provider url"  <env-entry> elements at the bottom of prweb/WEB-INF/web,xml

The actual JNDI implementation, i.e., "service", is vendor-specific.

prweb is a client to the JNDI service that is provided by the web/app server it runs within.

EX:

    <env-entry>
        <description><![CDATA[Tomcat/JBoss JNDI provider factory]]> </description>
        <env-entry-name>pega/tomcat/jndiProviderFactory</env-entry-name>
        <env-entry-value>org.jnp.interfaces.NamingContextFactory</env-entry-value>
        <env-entry-type>java.lang.String</env-entry-type>
    </env-entry>

If there is a possibility, suggest alternative solutions to client like REST or SOAP. Things will be a lot easier if we use industry wide popular methods.

JNDI is really a  standard API for "directory lookup" service to managed objects.  Generally we put different type of objects in JNDI (even X509 certs).   Queue/Topics are usually put there by MOM providers, so that we can all get to them via standard JNDI API.

JNDI is used to standardis access to LDAP for example where you can lookup DN entries etc. similar to how JDBC API is used for accessing various DBMS vendors, or JMS for accessing various MOM providers.

LDAP is an example for JNDI service. Client, for example prpc, uses naming service(Ex.LDAP) to locate objects by name. JNDI services are always outside of pega. 

Hope it helps!